How to deal with like file names w 2 cam shoot

Well, the simplest way is to make sure you offload each card into its own directory. Secondly, it depends on what NLE you're using to edit with, and whether or not your NLE supports the AVCCAM metadata "user clip name" feature. You could name each user clip name for the camera (something simple like "CAM A" and "CAM B" and then the user clip names would be "CAM A 0001" and "CAM B 0045" etc.
 
I usually transcode AVCHD and change the naming convention.

Or, Premiere also supports dragging the MTS directly into the NLE....so you could copy just the MTS files to a directory, use Adobe Bridge to batch rename them, and then drag them to your project. Do this ONLY if you have clips shorter than the 25min clip limit, otherwise spanned clips may not work properly.
 
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