yes it has been working seemingly ok. So you are saying the requirement that BOse has stated that the speakers go only into the sub is not required? The sound works but I am not sure it is working as best it could be. Meaning would I be missing something in sound quality if the speakers bypass the Bose subwoofer?
I see now. Can you post a picture of what exactly the geek squad did. I just looked up your bose system and I'm not sure how they managed to connect he speakers directly to the receiver.
By connecting the speakers to the Bose subwoofer I'm guessing there is some proprietary crossover or sound mixing going on.
In either case, whether Geek squad messed something up, or if you've got what you've got, my own personal opinion is that you're never going to get great sound from that system. Perhaps not even good sound depending on your own preferences, but that's just me.
A picture of what Geek squad did exactly would go a long way in determining whether it's them or the speakers. Do you have the original wires that came with the system to hook everything up to the "subwoofer"? You may want to try that and see if it changes anything.