To me, the most important connection you need to make is from the BR player to the receiver so you can get surround. Does your Onkyo have an Optical Audio-In connection? It should unless your receiver is more than 8 years old. So:
1) Connect the HDMI from your BR player to your TV. This will give you 1080p picture and it will send audio to your TV speakers.
2) Connect the Optical Audio-Out from your BR player to the Optical Audio-In on your receiver. This will allow you to get full surround audio from your discs.
None of the above should affect how you have your Bose speakers connected.
I have an old (old!) Onyko receiver DS-TX656. I just purchased a new Samsung 3D TV and Blue Ray player. Yes I should go out and buy a new receiver but right now I'm totally confused about how to set this system up. I have Bose speakers attached to the Onyko for surround sound.
Can someone give me some detailed instructions on how to get this configured?