Subs:
If your sub isn't working properly check the following:
Phase: most aftermarket head units offer you the options of "OFF, NORMAL, REVERSE" Try switching between normal and reverse and see which sounds louder.
Bass boost: Turn it all off.
EQ: Turn this off as well if you have a loudness function.
Gain: Leave your HU's sub setting at 0, then adjust the gain of your amp so that when your HU is set to the highest sound level you will want the speakers at, turn up the gain till the sub matches that sound level. The proper way is to adjust it until it starts clipping but the only way to tell is if you have an oscilloscope, kinda expensive piece of equipment though.
Position: In our cars, facing the sub towards the rear of the trunk and having the sub within 3 inches of the rear of the trunk will produce the highest SPLs granted the pass through hatch is open. If not, SPL will suffer. If you're looking to gain some of that back, removing the rear 6x9's will help a little.
Try moving it around the trunk and see what works best for you.
If all that fails? Perhaps you need better subs....