Can anyone recommend a way to convert my NEX-6's .mts footage to something which Mocha supports?
I'm using the version of Mocha that ships with AE-CS6.
There's several AVCHD/.mts converters available, but I have no idea what one/s is/are good.
What should I change the format to? And does the process deteriorate the picture quality ?
mocha only handles image sequences and Quicktime, most of which you can produce directly by just rendering and reimporting your stuff into AE. As long as you use formats that don't add another level of compression, the footage won't get worse.
Mocha can handle uncompressed AVI. See this webpage on Mocha supported file formats (valid for version of Mocha shipped with AE CS6 as well).
However, since what you want from Mocha is just tracking data, and you don't have to use your transcodings in AE project all the time, you can transcode your MTS files into something compressed as well. Personally, I was unable to see any difference in both tracking quality and time between QuickTime H.264 and TGA. Since then I transcode AVCHD footages to QuickTime H.264 progressive (in my experience Mocha handles interlaced files much slower) with maximum bitrate 17 Mbps, when I need to track them in Mocha.
Your experience can be different. So, test on your own.