here is my guess, but keep in mind its a guess heh. I think that when you turn off the subwoofer from the head unit, it cuts off the very low end frequencies to the rear speakers. And i think its the rear channel that the amp splits into rear speakers (L and R) and the stock sub. So to turn off the sub, they just cut off the frequencies going to it haha. I could be wrong but that would explain why i only get the low end when the stock sub is on. ( whether its hooked up or not )
As for why i spliced into the rear speakers, this is because ive had bad luck in the past trying to reuse the subwoofer output. I rather use a full range signal from my rear speakers and put a LPF on the signal for my subwoofer (its built into the amp). Plus it will give me better freedom as to where the frequency cutoff is.
Ive decided my problem atm is that my RCA cable is having problems so i ordered a new one. Hopefully after that, everything will work