After you have done the mind sweep and collected everything, you will process and organize. As for your projects, set up your Projects list before any project folders. You probably won't need a folder for every project. Let each entry on the Projects list be a statement that is true or false, such as "Summer camp flyer has been printed," "Finding has been secured for the XYZ program," or "Assistant program director has been hired." For each of those projects, you will have a next action to take. Keep those on your context lists (@Calls, @Home, @Errands, etc.)
You may also have some paper related to your projects. That is where the folders (project support folders) come into play. For instance, with the summer camp flyer, you may have sketched out several rough drafts, have a memo from someone with suggestions for inclusions in the flyer, and a quote from a couple of printers on the cost of duplicating your flyers. If so, make a folder called "Summer Camp Flyer" and put that sort of paperwork in there. Note, however, that all of it is reference material that is now located in a place where you can find it. The reminders of what to do are the items on your context lists.
The item regarding securing funding might need a folder to house letters for people who are pledging funds, a list of contributors, a draft of a letter asking for funds.
The item regarding an assistant might need a folder containing resumes or applications from potential candidates, a job description, or a salary schedule.
During the weekly review, look at your project support folders. You may find a project is now "Done." If so weed out the folder to see what can be thrown away, what needs to be filed somewhere else, etc.
Hope this helps,