Kind of surprised that no one answered, but here goes with my very limited knowledge.
You calibrate whatever input you are going to use to watch on your TV. So if you are going to use the USB connection for TV viewing, then you can calibrate through the USB connection. You would use the AVCHD mp4 version.
However, that wouldn't necessarily work for the other inputs, as they would need their own calibration. So download all the versions and have them ready when you get a DVD/Bluray player.
I used the mp4 version to calibrate my WDTV Live on input 1, then I used the Disney WOW DVD for my DVD player on input 2. If and whenever I get a BD player, I already have the AVCHD BD or the HDMV BD version to calibrate that.