heres my setup..mabey it will help
ok here is what i did... First of all i replaced my stock head unit with a kdc-mp-919. It has better equalization and cross-over options. I replaced all speakers in the car with 2002 kenwood excelon dual mag speakers. These speakers.......7 2ways in the front and the 6x9 3 ways in the rear trunk are powered off a 500 watt kenwood 4x amp. These 2 sets are connected via front and rear output rcas. The amp is slightly turned down in both the front and rear to match the other components and a lil extra in the rear to compensate for the dominace of the 6x9s. Aproxx wattage 30 front door panel, 20-22 watts trunk mounted 6x9s.
Then I added 2 more sets of dual mags, 2- 1 inch tweets flushmounted to my side paneling running with my windshield, and also 2- 6 1/2 mid range cones. These 2 sets are hard wired directly into the deck running at approx 22 watts rms each.
The crossover settings for the mp919 (head unit) are set so that the cross over channels are reverted into the rca outputs if there is a complete circuit on them. Therefore you control the 5x7s and the 6x9s via the head unit. But the 1 in tweets and the 6 1/2s are controlled via independant crossover networks.
This can posses a slight problem with equalization because of the dominant channels running out of the rca outputs, but remember the added speakers were only for soudn balancing issues rather that main music drivers. So i basically run my system using keenwoods custom eq manager integrated with the mp919 head unit.
As for the bass freqs...i have 1 kicker s12l7 in a large vented box powered byt a kicker 800 watt amp. this is connected to the headunit via rca non fading output..so it can be controlled by the head unit and be integrated with the internal equalization process.
Hope this helps with any problems you were having.