I think it's definitely a good idea to write a script down with a comic with a plot, although everyone has a certain process that they're the most comfortable with, so hopefully you'll figure out what way you want to do it. I've been working on my webcomic for a few years now and it just helps to have those scripts and outlines, because I still find myself changing things around or coming up with new ideas, and it's good to have the scripts as a reference of the timeline of the story as well. With the webcomic I've been working on, in the beginning I planned out a basic outline of what I want to happen in the story, and originally I didn't have an ending planned. Now that the story is coming together more solidly, I usually get ideas for different chapters and start writing out the script. My scripts are very loose and I write them immediately as I get the idea for them, so they're sort of like a steam of consciousness and not really formatted in a pretty way.
I usually write the actions in parenthesis, and then the dialogues. I don't differentiate which character is speaking because it takes up too much time, and I try my best to get that raw idea of what I'd imagined in my head onto the document. After the rough script, I organize how many panels I want each page (adding panel numbers into the script) and then figure out where I feel is the best place to end that page. Afterwards, I work on the thumbnail, and then the final page.