AppleTV vs. AppleTV 5.1 in VisualHub

I have started to use .mkv files and I had a question about converting a .mkv file into the AppleTV format using VisualHub. I noticed there were two options I could choose from, AppleTV and AppleTV 5.1. When I choose AppleTV it stores the file as a .mp4 file. When I choose AppleTV 5.1 it stores the file as a .mov file. Which is better to use?
One more question, when you do convert formats do you use standard, high, or the go nuts preset?

thanks for your input.