For Tivo purposes you can preserve ac3 5.1 audio as is and transcode to h.264 video. However be warned that since ac3 audio in mp4 container has only recently been ratified some players can't handle that yet. For example Quicktime and Windows Media Player won't play mp4 with ac3 audio but recent versions of VLC do. So if you are targeting other means to play back those files other than Tivo you should check whatever players you plan to use to see if they can handle it. If you use 6 channel aac audio instead that would make it compatible with most players but not sure how Tivo outputs 6 channel aac as far as surround sound goes.