The headunit's power output is totally irrelevant when you have a BOSE factory system. The installer that put in your headunit used the line outputs if he installed it properly, or he used a line converter if he was lazy. Either way, the power from the headunit isn't being used at all.

Your best bet is to go back to the BOSE(as in the original headunit) or finish the job(replace/remove the BOSE amp and replace the BOSE speakers) - it will probably be several hundred dollars to get the speakers replaced and have your installer pull the BOSE amp entirely and wire the speaker directly to the headunit. After that, get a small 200watt class D amp to drive the bose subwoofer.

Also, there are several members in AHQ who can probably give you a better quote on the labor than your shop would. keep in mind you have a 8 speaker system so you will need two sets of components, coaxial speakers wont sound as good.