I have the same setup...I have a HD DVR from the cable company and a SD Tivo Series2, both of them are hooked up. There are two points that we need to understand in order to hook everything up correctly:
First, if you run video through the Tivo but audio bypasses the Tivo, you will notice a time lag between the video and audio. This is because the Tivo processes the signal and records it to the harddrive, which allows you to rewind. Therefore, the audio will be about a half-second ahead of the video. Therefore, you either have to run BOTH audio and video through the Tivo or NEITHER video nor audio through the Tivo.
Second, try this. Your TV probably has an audio out, either digital or standard RCA-based. This allows you to run a video/audio feed from the cable box to the TV and a video/audio feed from the Tivo and watch them independently. But, the receiver gets the audio from the TV audio OUT so you never have to change it.