I had a Bose system in my 97 Maxima, ripped it all out and installed aftermarket (long before I decided to build and install my carpc), but in the process of decision-making I learned about how the Bose system works. The HU sends out a very low power line level signal to each speaker, which are individually amped at the speaker. You need a line level converter (Scosche makes one, I saw it at Walmart) to attenuate the output from an aftermarket HU to the Bose speaker amp inputs. It can be done, but it doesn't sound nearly as good as full aftermarket system.
The "line level" is different from the Bose than normal, I believe the Bose is higher level. Read here:
And for even more info on Bose systems, look here: