How do you brainstorm your plot/script?

I’ve decided that I’m not going to make episodic issues of my comic book anymore, as the story has become too thick and involved to split up every 24 pages. I’m going to work on everything beyond issue 1 (which is now the prologue) as one single, unified graphic novel. I have a vague idea of my story arc planned out, and I used to plan out each comic script in terms of how many pages I’d devote to certain elements.
However, this doesn’t seem like something practical, now that I’m starting a script 24 pages in (issue 2 is now the first few pages). The comic was going to span about 20–30 issues, but now it’s going to be even longer due to lack of space constraints. How does anyone work on a script that long?
I mind[bubble]-mapped my character relationships, but bubble maps also seem impractical for linear plots with sub-plots branching off. Ideas? Suggestions? Concerns?