Pass-through audio in Encoder?

I am wondering if it is possible to take a file with multiple video channels and transcode it to a new file type while retaining those seperate channels?  For example, I have a lot of mp4's with 4 audio channels and I want to transcode them down to mov's while keeping the 4 audio channels seperate and not mixing them to stero or mono.  Anyone had any luck with something like this?