You do not need to turn off your internal speakers.
If you have a regular home theatre setup, it would go something like this:
Cable Box or Satelite Box - Audio Out (digital or analog) to your Bose input.
You do not need to use the audio out on the TV at all. You can just lower your volume on the TV and listen to your Bose System, or leave the Bose System off to listen to just your TV.