It's not all that hard to change out the headunit, but if you want to keep the stock speakers and amp you will need to get a line converter to hook it into the stock amp. Since all the signal processing is done in the BOSE amp, why would you want to that anyway? It would essentially sound the same, but on the upside you'd have the modern technology (satellite radio, USB drives, iPod, etc...)
However, if you hooked the aftermarket headunit directly to the speakers you could get better sound quality, but should make sure the head unit can handle it. The BOSE speakers are .5 Ohms while most* aftermarket speakers are 4 Ohms. I can explain this WAYYYY in depth to the point I think only Phen would get, but let's just say less resistance = more amp = More load on the headunit.