Here's how I use Folders (as everyone is different, most others will have something totally different):
[1. Objectives] - these are all my projects/actions directly related to my immediate job objectives as outlined in my annual review. These will advance my career.
[2. Production] - these are all my projects/actions directly related to my job as outlined in my job description. These are why I get paid.
[3. Administrative] - these are all the projects/actions directly related to the daily administrative tasks that must be done but don't directly relate to my specific job. We all have these.
[4. External Committees] - I'm on a lot of these, I work for a public authority and represent that authority on a number of city/county/regional committees. These are important but do not relate directly back to my job description.
I have these numbered so that they show up in my order of importance. I try to focus the early part of my day on Objectives, then Production. The afternoon, when I'm fried, I look at the mundane administrative things. Committee actions get done in between or in the evenings.
Obviously these 4 folders are work related, I then have a few for Home/Financial/Personal. These are focused on when I am at home.
Hopefully this gives you an example of how folders can be used. By setting things up this way it makes it easier to develop specific Perspectives to work from during your "do" time.