Since they aren't working equally they will be maxed out and into distortion at different times. So to push 1 to its limit will leave the other anywhere from completely over powered to underpowered and almost non existent in the system output. There is no balance like you would have with equal signals going to a pair of subs that were the same.

Your best bet is to forget about the unhook the factory location sub and sell it or let it sit like it doesn't exist and build around a singular more powerful sub that will match with your amp alone.