Omnifocus is a flexible tool that allows you to keep track of your commitments in a variety of ways.
I think the key point when implementing your GTD system is to make a firm delineation in your mind about what is an Area of Focus and what is a Project. This helps you to know where to put new things as they appear and, perhaps more importantly, know where to find them again when reviewing and doing. There are other threads in this forum that go into this, but I currently make distinctions on the basis of scale.
For example, an Area of Focus in my job might be Sales; this might be subdivided into smaller Areas of Focus such as Italy etc. Projects start to appear in within these as things like "Sell product x to organisation y", within which there may be sub-projects such as "Research requirements" etc.
I'm with Oogiem here, in that I currently use folders in Omnifocus for Areas of Focus and Projects for...well, Projects. Sub-projects come in as grouped next actions, since Omnifocus doesn't have an explicit entry for these - but the end result is the same. I also prefer a flatter folder structure - no more than two deep for a particular job - so that things don't get too prescribed.
And as Gardener says, you only need to enter an end date if there really is one. Otherwise, the GTD 'textbook' recommends simply completing the next actions within a project as soon as you can (having looked at everything in your world and deciding on the best thing for you to do at any given moment - easy huh?!).
If you enter end dates simply to help you prioritise (i.e. the project or next action isn't really dead if it goes over that date), then you'll find you have a whole heap of overdue items flashing at you and tugging at your psyche. I know, I have this issue myself at the moment...
Good luck with it all!