What program are you using?
I use Photoshop, and my method is to put the lines on it's own layer- since yours are scanned you can make it a multiply layer and put the flat colors on a layer beneath. I usually do my flats on multiple separate layers (one layer of skin, one of hair, one or two for clothes, etc) then I lock the layer (lock button on layer menu) and use a painter brush to paint and blend my shadows and highlights. You can still use overlay and multiply to enhance shading and lighting and what not, but I like the painterly effect I get through my method.
I use clipstudio and uhh depends. You could render till the end of days if you wanted haha. Though my coloring process for characters (tend to paint bgs for that animation look) usually goes like this:
- flats
- painting (so like around the nose area and what not
- multiply layers for shadow
- so lineart - make a copy, set it to overlay, and then use the other for hue (though I'm lazy and use gradients lol)
- glowy whatever (glow dodge or add glow for example) for highlights
- then overlay layers for more hue stuff so that it fits more with the background
- then the whole panel gets a multiply and screen treatment
- gradient map and texture and blur anything that needs it
Sorry my process is so long lololol, took awhile for me to figure out what I'd be satisfied with. I'm working on some panels rn so if you want I can show you the process with pics?
I do everything on my ipad in procreate. Luckily the style for my comic is very simple so I can most of it on one or two layers!
One thing that I have found very helpful is a I have created a color palette for each character so I can quickly grab the same color each time.
1.)Flat Colors - Usually one layer for characters and one for the background
2.)Line Work (darker shade of the flat colors)
3.)Add highlights or shadows if applicable
(1 & 2 are usually on the same layer - with 3 on a new one - unless I'm being really lazy... which happens more often than I would like to admit)
I may use a another layer if I want to add effects like a blur.
I usually do a layer for base coloring, and 'clipping layers' (if you use photoshop, the function exists basically in all photo editing software) for shadow/ shading.
I personally just pick a complementary / darker color for shading, and don't mess too much with multiply / overlay because sometimes when you compress layers the effect messes the final product D: I also just do cell shading, so it might be a bit different.
There's tons of art tutorials online that are a huge help/ motivator, so my advice is pick some of your favorite artists and see if they've done tutorials in the past!
heres a really really old process gif from 2016

purple coloring is on multiply, the highlights were add/luminosity layers
my style nowadays is more complicated, i separate the background and characters entirely with their own lineart and shading layers on multiply, i use overlay and a soft brush to add more depth to the character layers with yellow/purple coloring and i add a gaussian blur layer to the bg when the characters are the main focus. i also add an overlay layer with one solid color over the whole page for dramatic lighting, and use add/glow layers and a soft brush for atmospheric lighting
i usually end up with something like this

the folders are for character lineart/colors and bg line/colors
the hell is that my dude!
colouring comics is very much a case-by-case basis. theres a (hopefully dying) marvel-dc industry standard - which consists of being complete ass imo, not worth learning. every comic and every art style deserves a different approach to colour.
myself, im in a lot of transition colour-wise. but my most basic approach is picking like 3-5 colours and slapping that shit down with various textured brushes and the pen for smooth application, and then adding some hard light and soft light layers for some contrast and a nice sexy glow. im very slapdash 'pretty and emotional > accurate' kinda colourist right now, although i havent always been.
some examples:
but also, heres the colours for another comic im working on:
now theres similarities in how i approach gradient, contrast, and blending, but this is veeery different right? mainly bc this was a linocut print, and the others were drawn in csp. this is just an example to show how colour can be done very differently depending on the demands of the project.
- Background!
- My 'base colours' I start with a darker shade because that makes painting in the lighter colours much easier while also giving the drawing more depth than when you start with a light colour and go darker.
- Painting in my characters skin and hair tones, painting light over dark base colour creates softer shading. I don't try to make it near or perfect because I know I'll be adding hard shadows and lighting soon.
- Adding Hard shadows based on my light source on a Multiply layer and airbrushing some soft highlights on an overlay layer.
Everything is like speedpainted and not really meant to look too neat, I don't exactly do flat colours either because they're so time consuming
I think you should use one page of your comic and colour it in a variety of different styles, experiment as much as you can! you'll be able to compare the different styles at the end and maybe figure out which one fits your comic the best.
I practiced different colouring styles before starting the comic and when I found out that using a darker base and adding highlights makes shading sooo much faster and better it helped me a lot, I even implemented that in my regular art. It's so much fun to paint like this and colouring is always my fav part of my process especially if the scene has some dramatic shading.