It's important that project plans are separate from your next action list. I have large projects, and have to do a lot of formal planning, and find that once I've done the brainstorming I might end up with many parallel open loops for the one project and therefore many next actions per project, as well as many projects all going on at the one time. So when you are generating the next action or actions for the projects, you look at your project plan and decide whether to put a NA for all of the open loops, or maybe just some of them (in order to keep the NA list to a reasonable amount of actions).

I have one NA list in an iPhone app (Pocket Informant) that allows sorting by context, and also viewing by project.