It seems to me you're making it harder than it is, but that's up to you.
I'm on my third mustang with the shaker 500. You can do whatever floats your boat but this is my recommendation:
Upgrade the front door speakers. Factory speakers are weak and flat sounding. The rears are even worse. I've had subs in the 2012 I had. Even at low volume, standing outside the car, the car is a rattle trap. If you want to spend more money on Dynomat, or enjoy embarrassing yourself with your car rattling like a $ 500.00 Honda, go for it. I opted to change the front speakers and amplify the rears. They will sound much better.
You can run a 5 channel amp that will solve all of your issues. Or you can run two amps, line out from amp 1 to line in on the 2nd amp for subs. All you need to do is cut into your rear speaker harness, connect your LC2 converter, feed it into your amp and you have your rca output for your amp(s). Then send your audio feed back into your rear speakers from the amp. It will drastically improve the sound of the rear speakers and you'll have a more balanced sound.
If you think that the factory sound level of the front speakers (once replaced with good aftermarket replacements) is low, or not loud enough you have hearing loss. I replaced the fronts with infinity's and at 75% they are loud enough to hurt your ears. Good luck.
It is better to remain silent and be thought of a fool, than to open your mouth and remove all doubt.