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.
This is exactly what I'm wanting to do. I like the "surround sound" effect. I've changed all four of the 5x7's to Infinity's, which was a major improvement, but the rear speakers don't put out much volume or bass. So basically the only wires you have to run to the rear is the power wire for the amp because all of the other wires come off of the rear speakers. Is this correct or am I missing something?
2014 Ruby Red V6 Premium w/pony package, Magnaflow Street axle-backs, LED license plate light, LED interior lights, Strip LED trunk lights, MMD Hood struts, SCT X4 Tuner with Steeda tunes for life, Boss 302 strut tower brace, OEM extended range remote start, Raxiom Navigation.