If the 5008 was able to ping every speaker and the sub, then complete without errors, you should be set. Are the sub and surround channels not getting any sound at all or are they just not loud enough?
The starting point should be some kind of demo material that sends test signals to every channel individually. Some BluRay discs have a test like this. I cannot remember a disc off hand, I believe Avatar BD has it. I believe any BD optimized for THX has the audio/video optimizing guides. So, look at the back cover to see if it is included. If your system passes sound to each speaker/sub correctly, it is just a matter of adjusting levels to your taste.
Regarding lack of bass, if the subwoofer is correctly set up, it should not betray its presence. If it seems that all bass is coming from L, C, R, the auto calibration setup did a good job. If you like more bass, try Audyssey Dynamic EQ on. This should work the subwoofer much harder.
Regarding lack of surround sound, it is possible that the mix did not have much content on them. (I find that hard to believe for The Hobbit though.) You can go into the speaker level settings and turn up the individual trims.