I think I found a flaw in your tuning process. Pehaps try this series of steps:
1. turn off the subs in the rear, set bass & treble controls on the deck to center and set any eq's to a flat or bypassed setting
2. set the high pass filter on the amp for the front at about 80-100Hz.
3. start with the gain low on the amp and the deck volume at about 90-95% of max volume
4. play normal music, not super bass-heavy stuff, and slowly advance the gain until you hear the speakers distort a little and then back off the gain a little.
At this point you should have fairly balanced sound up front, missing only the lowest frequencies. If you think it sounds a little thin, try flipping the + and - wires for just the right speaker and see what changes. If the sound has even less bass, change it back. If it has more, keep it that way. (actually a better way to set this is using a relative polarity check from a disc that has the special tracks on it)
5. now set the low-pass filter on the sub amp no higher than 80Hz with the amp gain all the way down.
6. while playing normal music at normal to slightly above normal volume, not super bass-heavy stuff at high volume, have someone slowly turn up the gain on the sub amp while you sit in the front listening to the change in the system. Keep turning up the gain until the bass from the subs fills the sound of the system without pulling the bass to the rear.
Then the real tuning can begin. :-)
Let me know if you have any additional questions.
