So, doing a search for “Sixaxis” here on the site gave me a post with a bunch of random links. Using the “Command F” function and searching “Sixaxis” on the current page gave me one result, and I found one link that contained the word:
http://mypiandi.blogspot.de/2012/12/retropie-sixaxis-over-bluetooth.html
The title and content of the page give me reason to believe that you CAN use the Sixaxis controller with Retropie. Now only my bluetooth related question has yet to be answered…