actually wiring high level outputs into the low level inputs of the BOSE amp greatly reduces the sound quality and messes up the crossover points. Since the bose speakers are perfectly matched to the bose amp, changing the crossover points makes a decent sounding system sound horrible.
I guess I wired mine in by matching up the colors and it sounded fine to me, and my friend has one wired in like that and it sounds fine also. But personally I would splice in the RCA's if you are keeping the bose amp.