I don't know about the Bose headunit, but the Base headunit has the front and rear speaker output in two different harnesses. In both harnesses there are other wires for other connections. So unless you rewire all of the wires on the harness back to the vehicle, you probably will find something not working. I just found it is much easier to cut the 4 pairs of speaker wires from the two harnesses and solder directly to them. (Apply heat shrink tube of course, don't settle for electrical tape. They will fall off and give you short.) If you ever need to take out your amp, just cut the wires and re-solder them. It takes only a few seconds to solder a joint, and they are hidden behind the headunit anyway, so it wasn't an issue to me.
Regarding the power line, if you plan on to add a 2nd amp for the subwoofer, a 4 AWG is a good choice as you will need to share the same power line for both amp. If you plan on to have just one 4 channel amp, then an 8 AWG is very sufficient. The smaller wire is easier to hide under the door trim, and it fits perfectly on the clips on the top of the plastic channel on the driver side, giving it a nice separation between the speaker wires inside the plastic channel and the power line. I think the clips may be designed for the factory Bose amp power line.
The space of the factory Bose amp location is not very big, so you probably want to measure your amp to see if it fits. Mine is about 10"x15", and I can barely fit it in there without interfering with the folding down of the back seat. It was so tight that I had to cut a corner of the custom board off to make it fit. If you amp is wider or longer than that, you may have a hard time fitting it in that spot.