I think I've made a mess of my set up.
Installation and Configuration
For now I would recommend NOT using Site Builder. Until you get a handle on how Jamroom works, trying to "design" your site is just going to add more complexity when you don't need it.
You can do a full reset of the system as the master admin go to:
ACP -> Tools -> Developer Tools -> Tools -> Reset System
After that go to ACP -> Skins -> NingJa and check the "active" checkbox and make it your active skin.
Then re-run the Ning Import.
The important thing at this point is to begin understanding how Jamroom works - once you are comfortable with that THEN move on to more custom and complicated tasks.
Let me know if that helps.