:-) I'm afraid if you don't know how to explain what your question is, no one will be able to answer it.
I'd suggest that you start by watching the tutorial videos
here. If that doesn't answer your question, it may help you reformulate your question so we know what the problem is.
If you
do still have questions after watching the videos and want to try asking again, it might be helpful to describe an example of a project and sub-projects, and which parts you are currently using OmniFocus for. Even better, you could include some screenshots to show what you're doing. Believe it or not, it is really hard to tell what the actual difficulty is from what you've described.
You could also try contacting the OmniGroup support gurus by
email or phone (+1-800-315-6664). There's also a guy who indicates in
this thread that he might be willing to screen-share with people looking for help.
OmniFocus is designed to have the flexibility to manage and keep track of complex projects. You probably won't need any hacks or work-arounds once you understand how the software works. Watching the videos will give you a good start.