If I think that a part doesn't work or the characters aren't acting right, I reread and think over the scene in my head with a few changes each time, I keep going like that and bounce ideas around until I find something that feels right. As for Dialogue, I flat out have to say it all out loud. It makes me come off as crazy but it sure does work.
For me (when I'm writing for my comic) it's like watching a movie in my head. I'll daydream the scenes and what the characters say/do - if it's good I'll note it down/sketch it - and if it's crap, too dark or totally not canon to the main plot... well, at least I enjoyed myself for a bit. 
I do have to watch my characters actions and dialogue, because you are right - they have their own personalities and it can feel wrong to make them do or say something out of character.
Even with drawing - I have issues when drawing Genii smiling, because he doesn't do that often in my story. It's like a betrayal. 
Whenever I'm scrap for character dialogue or unsure on how they would react, I do one of 3 things:
1:Imagine the comic in question as if it was some degree of cartoon/movie/television show, and see how delivery and pacing would work in a non-comic format to get the idea of how characters would work on brevity and such. Word balloon breaks being gaps in the delivery, for example.
2: Read the dialogue out loud to myself and see if everybody sounds same-y or not. Usually in the car or when I'm alone so I can get inflection and emotion into it to see if they sound the same regarding it.
3: Go back to whatever prior character/characters the person I'm writing is based on as a comparison. (What would James from Team Rocket say here, as an example.)
Those usually work for me!
So, it feels more like you treat them like a puppeteer or maybe like pawns on a chessboard, doing whatever you will them at your own behest, right? Like an omniscient overlord (which, I guess we technically are), you put them in the places you feel work best regarding specific situations. It feels like you're playing chess and analyzing how one pawn would match together with other pieces to make for a good and thrilling game. I like it!
Hah, so should I start calling you an asari? It's like you're mind-melding with your characters. Or, I guess it's just the ordinary, "were I in their shoes, what would I do?" It makes sense -- absolutely nothing wrong with that.
So, your method is like reading a play aloud to see how it would sound when done at x time in y situation?
Fiction is usually based off of reality in some format -- if you think of it like talking to a friend you're close to, is it really so off base?
There's nothing crazy about your methodology. Some things just have to be heard to be really focused on. Well done on finding something that works best for you.
I tend to have movie scenarios enacted in my mind as well, but then I typically want to physically encapsulate everything that goes on, and that's just asking for some injuries.
When you go about creating your comics, do you do dialogue first or imagine the scenario first and fit in the dialogue to match?
I imagine my characters as "people" and let them essentially behave as such. People are really fluid when it comes to the way that they talk and behave. Hence why people have "multiple sides". I'm a very shy person though I often appear very confident. I didn't learn until my senior year of high school from my dance teacher that I'm only "confident" when I'm comfortable. If I'm in a new situation, I'm very quiet and reserved. My brother appears very strong and confident but will get really flustered if he isn't able to figure something out first.
I think it's important to define your character's relationships' and what's considered "normal" for each one. Characters should have the option to present themselves in different ways depending on the scenario. One of my characters has a brother/sister relationship with another character and they quibble all the time. We see different personality traits come forward depending on who he has a scene with.
For another character, I defined that one of my characters was most likely orphaned or at least a runaway. She decided that she really wanted to bug my assassin character. That later revealed to me that she was desperate for a parental figure. The assassin goes from barely tolerating her to "Papa Bear" mode because she's now his kid.
As a couple of people already mentioned, I think it's helpful to imagine being in the character's shoes and learn of they feel and think about things. Not just look at them from an outsiders perspective, but understand the "inside" 
No idea if this is helpful or not, but I find it much easier when each character has a unique "energy" or "aura" to them, that is different from each other. That way, you don't have to know every detail about the character, but can still get an overall idea and discover details later on and still keep everything consistent.
This reply made me laugh, because... yeah.
I used to think that characters having their own "will" and "voice" was normal!
.......
And then I got diagnosed with Dissociative Identity Disorder.
I usually role play in my head a scenario for my characters or even roleplay as them in real life with figures. I think the way @Legendofgenii is identical to my method:
I daydream quite a bit and that's usually how to get my ideas of episodes and what my characters would do and what they would say in that episode. It's fun and as you said, it's "like watching a movie in my head." That's exactly how I see it. I think it's a wonderful tool to use especially if you're bored, no harm in being lost in thoughts, unless you're supposed to be doing something important xD
Yay. Samesies. 
@Kylano My husband tells me off for scowling, smiling or looking worried whilst staring at nothing - and It's usually because I'm thinking up some over dramatic scene in my head. I don't tend to physically act them out - unless I can't find a good reference for a drawing. 
I get a good feel for their personality first and whenever I write their dialogue or them in a scene, I imagine myself as them or talking to them. I aim to keep them consistent whenever they’re in a scene and think how they’d react. If something feels off then I tweak it til it feels right. I never thoroughly plot dialogue so I let it flow naturally when my characters are having conversations.
Fiction is usually based off of reality in some format -- if you think of it like talking to a friend you're close to, is it really so off base?
No, my characters are not my friends. My friends are sentient beings that is real outside my mind, their existence and interaction is independent to mine, they are people not some figment of imagination.
For analogy imagine you have a cute doll. You like it so much you gave it a name and think what if it has a certain personality, and started to build a story revolving
around it. Then based on your imagination and constructed personality for it, you started to think how it will interact like a person. You tried to talk to it and ask questions, and you imagine it answering based on personality and traits you give. You even thought your imaginary conversation is like those of friends. All good, aren't all character owners are like that? Nothing is off limit to me.
Unless you really think the doll answers it itself and it is the actual doll answering, not your projection of its personality. Or you think The doll is a real sentient being that its sentience can be independently exists apart from your imagination. Now those are terrifying and off-limit to me.
I hope I did not offend anyone who are psychologically different, such as having DID. Yet, my characters gaining sentience in my head then taking over the last remnant of my already fallen apart (and probably near-inexsistent) sense of self and personality is one of the things I am fearful of.
Voices from my dreams whisper into my ears prophesies. Horrible predictions, all made by the angry spirits.
No worries, no Annabelle happening here. What I was referring to is like how people use animals in an anthromorphic manner, where they suddenly talk and display human like expressions/gestures. We know they're cats and that they can't speak as we do. No doubt there. But I've never needed to have such a clear barrier between reality and a cognization of something that doesn't actually exist anywhere but in your mind.
No, your characters aren't your friends. That's fine, but typically, people base their characters off of experience of things they relate most to. For example, cooking manga might pop up because of this interest in cooking, not because they themselves are cooks. It's just something to base off of real-life experience, and on that note, I was asking about whether the characters you make are constructs that don't rely on actual experience or that they may be based loosely off of real people.
Phew. I almost thought it is another horror story.
To answer it they are amalgamation of traits and tendencies I have seen in people, sometimes exaggerated and sometimes downplayed.
Not offensive at all!!! It's actually extremely refreshing to see someone with this viewpoint. A lot of roleplayers try to co-opt DID and claim that you can actually make it voluntarily, and it's extremely harmful and toxic.
If your characters talk to you genuinely autonomously, I recommend seeing a therapist, as DID is caused by trauma prior to the age of 9 (or 11, in rare cases happening with comorbidities of ADHD and autism/ASD). Even if you don't remember the trauma (which is likely, as DID is extremely covert and is supposed to make you forget it), if your characters are talking to you, see a professional!
Also, there's a lot of fun and cool brain science on the weird things that roleplaying can do to your brain chemistry! I recommend this as a read on the topic! Actors getting into character has a genuine effect on electrical pathways in the brain very similar to the changes observed with identity disorders like BPD and PTSD, so it's fair a lot of people get them confused.
Also, as a psychology major and someone who's extremely well-read on the topic... don't worry - this is physiologically impossible
DID must be developed with severe trauma between the ages of 6 and 9 and cannot occur later in life! Anyone who tells you otherwise is severely misinformed at best, and maliciously trying to take advantage of you at worst.
Dialogue has always been on of my strong suits when it comes to writing anything, so I've never really thought too hard about it. However, I found that after a while, you just start to get to know your characters well enough that you know how they'd respond to certain things. I'm also not afraid of letting my characters surprise me sometimes, as occasionally I'll be writing dialogue and my brain be like "this character would totally act a little off in this particular scenario because of this particular character trait/or other person being around"
I think over all if you have strong enough characters with vivid enough personality, the dialogue eventually comes out of them pretty naturally.
I approach characters like people, what they tell you is who they are. And its takes time to figure out who they are. Typically when I do this, I draw an image of them, and then write whatever comes to my head. Or i will stare at a drawing I made of said character, and just think about who they are, and what they are like. I think of story ideas and then write them down.
its not as if the character it actually talking to you, but rather the ideas start welling up in your head, and their 'voice' is actually your brain getting ideas.
I try to put a little bit of myself into them so it's easier for me to understand what they would and wouldn't do, think, and say. I also give them character arcs personal to me so I know the natural progression of their arc from beginning to end.
I have one character who deals constantly with his own anger and stress, so much so that it drove him to commit a brutal murder, and he has a friend who is upset by this fact and feels concern for him. They both resonate with me (not the murder bit obviously) since I've felt uncontrollable anger and unrelenting stress, as well as concern for a friend's mental state. I try my best not to write about things I haven't felt or experienced myself. That's a little difficult tho cuz I like writing bizarre fiction
