Let me be sure that I have this correct.
1. You are running the 12 AND the 6x9's off of the 150?
2. Are you using a crossover?
If the answer is yes to the first and no to the second then I think I see your problem. Running a system like that is OK but not desirable. Remove the 6x9's from the amp and run them to deck power or another amp and get a crossover. The 150 should be plenty of power. Also, is the box just sitting in the trunk? If so, you might try different firing positions. Point it back, front and to different sides and see which one sounds better. The best would be to seal it to the rear deck or rear seat but with a 12 you would have a hard time and you would probably have a hard time getting the spare back in.