I assume you are referring to ctivo? Let me lay down a little groundwork and I hope I don't make any mistakes with the details here. The files on the Tivo are encrypted so when a program transfers the files to your computer they have to be unencrypted in order to be of ANY use. Next, the files are basically in Mpeg2 format which is not playable by all devices. For instance, quicktime doesn't support it. Further, files of this type are generally pretty large. So, you usually want to convert the files to a different format which is something that is part of what ctivo is designed to do. The problem is that most of the "built-in" encoder formats (like all the ones that start with 'Quicktime') are set to downmix the surround audio to stereo audio (2 channel). But I've found that some of the Handbrake encoder formats that are included in ctivo (like the 'AppleTV' one) do preserve the surround sound. Unfortunately, comskip doesn't work with them. So, I'm still working on a way to make this happen.
The most foolproof way to preserve the surround is to download the files with ctivo using the "decrypt" option which simply downloads and unencrypts the mpeg2 files, preserving whatever the original content was. Then, you can convert it to another format with the stand alone Handbrake program using a custom preset that enocdes the audio in a surround format (instead of downmix).
If you want automation, I'm still figuring that out. It seems that there should be a combination of option codes that will encode in surround but also work with the comskip function but I'm still stumbling in the dark on that. Another thing I'm working on is recreating the "decrypt/copy" format that itivo had. This format worked the same as the regular "decrypt" format except that it allowed the comskip function to run on the resulting file. (And it has the side bonus of making it 20%+ smaller on account of the commercials being removed) For some reason ctivo doesn't have this format built-in and borrowing the options from that format in itivo isn't working for me yet. The idea would be to use the 'on the fly' transcoding that Plex does to convert the mpeg2 format to something that my Chromecast can support without having to convert the file at the ctivo stage. The other hurdle is that this requires a fairly fast computer. My older core 2 duo (2.5Ghz) isn't quite up to the task but I think an i5 or i7 might be alright.
