Supernotecard to begin fleshing it out and breaking the story into single comic issues (chapters), then I'll jump into either Montage or Celtx for the final script. Unlike some writer/artists, I do write in full script format, and I do prefer writing the entire series up front before anything gets drawn.
In some ways, this new project will be an ongoing, but more of a series of miniseries. So it's important for me to set up a few story points that will continue through the various storylines, but still allow each miniseries to stand on its own as a complete story. In many ways, it's the way novels are written, a format I enjoy much more than soap opera style ongoing comics that never have a hard ending. But as always, my plans could change and the project could evolve into something completely different. That's why I'm reluctant to talk about it too much until I actually know what the finished comic will become.