I would suggest sourcing the higher level files if possible, and retaining the original file structure. If you can't source them, at least bring in what you have via Media Browser. Sometimes where a single MTS take has spanned across two clips Premiere will import two files into the project that are the same exactly. Just double check they are they same and you could remove one if it bothered you. Editing with MTS and movs will be fine, however to make Premiere work as smoothly as possible be sure to set your editing timeline to the format that the majority of the clips are in. For example, if 90% of the media is MOVS then grab one of the mov clips from the project bin and drop it onto the 'new sequence' button in you project panel and a new sequence will be created that will be set for optimized editing of MOVS.
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