So the amp breaks after a day or two when you get a brand new amp? If so. I bet the head unit isnt doing anything to kill the amp. Usually would have to do with voltage drop or having the subs hooked up wrong (not knowing the ohms are to low for the amp or something)
Now that the equipment is in the open, Input sensitivity + Bass boost = bad for the amp(s) Plus the boss amp may say its "Stable at 1-Ohm" but I doubt it is, look up the real specs via
sonicelectronix.com. If it's a phantom series, I know first hand it is not stable at 1-Ohm. It may perform (briefly) at 1-Ohm, but it won't last.
Not sure about the other amps. FYI 12.1 is a serious voltage drop, you're destroying your battery IMO.
RCA's could stand to be upgraded from your description. I've found shielded RCA's (Kicker KX-Line for ex.) don't pick up distortion. Distortion could be a factor, but I doubt that's what's killing your amps.
Inadequate ground + Input sensitivity set too high + Bass boost on + Substandard RCA's + Voltage drops = Amps inputs/outputs going bad.
Amps will power on, but no output.
Had a similar problem, only it was due to bad ground and a battery that's on its way out. This caused my inputs to heat up and separate the wire from the solder point of the input terminal. I was brave enough to open the amps up, found the wires separated, hit them with a dab of solder and they worked fine. I have yet to find a better ground or hook a system up since figuring this out. I recently made the jump from "Garbage" to Quality equipment. Was running an Audiobahn A1300-HCT (1400w Max, supposedly 1,1000x1@1-Ohm RMS.) Once the inputs gave out, I picked up a Kole Audio KX1-2000D (2000w Max, supposedly 1,000wx1@1-Ohm RMS.) Inputs gave out, posted in the sub-woofer forum suspecting my Subwoofer (Rockford Fosgate Power Series T1 12" D2 (T112D2)) was causing my amps to give out. Gave all the info I could, took pics of everything from my power wire to where my ground was bolted. Bad Ground + Battery on its way out + Amps that don't do rated power = Not clean power and amps giving out.
/rant
Hope the above helps. Best of luck.