You have almost the exact components I have. Here's how I set mine up and the reasoning behind it.
Sony Blu-ray DVD - I figured I would always want to use my Bose speakers when watching DVD's, so I went HDMI from the Sony DVD to my Onkyo 805 receiver. I then went HDMI from the Onkyo receiver to the Samsung 40 inch LCD. I have the receiver set so that it does not pass audio to the TV.
Charter Motorola cable box - I tried DVI/HDMI from the cable box to receiver, but there is an HDCP error due to the cable box. (You can find several threads about this issue). I could probably resolve it by switching to a Scientific Atlanta cable box, but I decided not to fool with it.
I usually watch TV without the Bose speakers. Therefore, I went DVI/HDMI from the cable box directly to the Samsung #2 HDMI. For audio, I went L/R from the cable box to the TV.
For those times I want Bose speakers with the TV, I went from the cable box to the Onkyo receiver with an optical connection.
This setup works great except that I have to switch the TV input and receiver input when switching back and forth between TV and DVD.
Also, I bought another Bose Acoustimass 5 off Ebay for my rear surround speakers. I'm actually running 3 Bose systems with 3 Acoustimass modules and a Klipsch subwoofer, for a 7.1 speaker arrangement. It works great.
One more thing...when watching TV, I have to turn the TV and receiver volume up or down, depending on which one I want to listen to. It's not a problem.