I have Bose Soundbar with wireless subwoofer, DISH box, cable box, Mac Mini and Apple TV. All my peripherals (both set top boxes, mac mini and apple TV) goes to TV and optical audio goes out from SONY TV to Bose Sound Bar. I also have Logitech Harmony 900 universal remote controlling all my components and everything works like a charm.
If your setup is similar to Mr. Patel's below, the audio signal would go from your TV to the BOSE system, so as long as all audio goes first to your TV, you should be good (you'll want to take audio/video signal from the Sony BD player via HDMI, single cable).
This player does have both coaxial and optical digital audio outputs as well as L/R analog (RCA) outputs so it should be able to support most home theatre systems. It has one HDMI output so if you are relying on that for both the home theater system and the TV, you will need both HDMI input and output on your theater system.