I have a video that I need to convert for usage on an apple tv. The specs of the file are as follows:
Video: H264/AVC
Audio: Acc-lc 6ch
Container Matroska

The video should be fine but the audio needs to be down enconded to 5.1 Is there an easy way to convert this to a new container without effecting the video and downconverting the audio?

mp4 is the container that you are after (somehow i don't think avi would work...), maybe remuxing is doable using mp4box (gui = yamb), but unsure.
http://yamb.unite-video.com/

note: there is a big chance video will have to be reencoded.