There is no standard method of using OmniFocus. It will bend to your methods. You may wish for a more rigid structure and OmniFocus won't offer that.
But you will gain much flexibility and power if you take the time to learn it. I think OmniFocus is almost like the martial arts. If you really want to excel in it, you need to take the time. Don't expect to automatically go up a belt because you wished it. You need to put some time into finding a workflow that will work for you.
A great place to start is this book:
http://www.usingomnifocus.com
Click on the resources button at the top to get a peek at some articles on using OmniFocus. Then the book is the real cash cow. It is worth every penny that I paid.