Some people use the folders in OmniFocus for Areas of Focus and have that work well for them. I prefer not doing that, as I often find that one project can relate to more than one area of focus. Still, I do use folders for some kind of high level topical grouping.
As for projects with subprojects however, I never use folders, but instead have either the subprojects in OmniFocus as separate projects, and the main project as a separate project as well (just as a reminder) or, more often, make use of the Action group functionality for the sub-projects, which gives me a better overview of the entire project at the same time.