I don't see your dilema at all. Your 4 speaker system sounds like any modern car. Simple. The small sub is obviously running with high-voltage to its dedicated sub - you can easily keep this or get rid of it.
Car audio is stereo. That's 2 channels. So any tuning beyond balance is accomplished by splitting those two channels. Splitting a signal from 1 to 2 leaves you with two idenical signals. It is not like a water tap where you get half the water to each. So I don't know why you'd be concerned about splitting out to 4 speakers.
A quality amp will allow you adjustments to tune without an additional crossover or dsp. To a degree of course. You can go with 2 2-channel amps or a 4 channel. There are numerous ways to connect either setup. You can do 2 paris of interconnects to the amps or 1 pair. With 2 pairs you retain fader control. With 1 you have to make all your front/rear adjustments at the amplifiers.
Don't know how much you want to spend, but the king of adjustments in the amp market right now seems to be JL Audio. Check out their amp section:
www.jlaudio.com
If you want to start a dedicated thread in the ICE section, go for it.
Bruno