I have a similar setup with a Bose Lifestyle 48 and a Tivo. I use the Bose remote to control the Tivo. The Bose remote is RF which means I can use the remote w/o line of sight and it will emit an IR signal to control the Tivo. Take a look at
[Link: worldwide.bose.com] and look at the section titled "Using your remote to control connected audio/video devices". It works really well. The only thing missing is that's there's no way to press the ThumbsUp and ThumbsDown on the Tivo but that's a small annoyance.