I am shooting on Sony EX3 and editing on CS6, pc version. What is the best way to format BPAV files into single, editable files for a client? I know there are third party options with Apple. I'm not that sure about the pc side, though.
You can't without quality loss. It is best to keep the BPAV directory as it is, including subdirectories. The alternative is to put all the clips in a timeline and export as a single H.264 file, with the generation loss and the drawback that it is one single file, which is IMO far more difficult to edit that the original small clips.
Use either the free download Lagarith or UT "lossless" codecs to export as *.avi, or alternatively the free download Avid DNxHD codec to export as *.mov.
All of these are designed for your purpose - export of files with as little loss of quality as possible (they are described as visually lossless) to a format which is accessible to a variety of NLEs and software players.
Yes, use Media Encoder. When you install the codecs, they appear in the Video codec list in AME.
As an example, in Format, select QuickTime, then in Preset select the appropriate HD one.
Now go to the Video Tab lower down the R hand panel and select video codec. Avid DNxHD will appear in the list which appears for selection.
UT and Lagarith will appear in the same place if you select .AVI.