Nikon D7100 and Premiere Pro

I have experience editing in Adobe Premiere Pro CS4 and want to upgrade to CS6. I have recently changed to using the Nikon D7100 to produce video instead of a traditional video camera. It is my understanding that Adobe does not directly support the .MOV files produced by Nikon. I am curious how many issues arise from such editing? I am an amateur user, will it be to complicated to conversions (do I even know what I am talking about)? Also does the quality of the video degrade as a result of conversion?

The files work natively in Premiere Pro CS6. Some users report that they get better performance when batch renaming clips to .mpg. Here is a thread: http://www.flickr.com/groups/nikon-d5100/discuss/72157630303565658/
It's the QuickTime wrapper which affects performance.

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