Here’s what i’ve been doing, though i’ve only had the cameras for 2 months.
Going into it, i thought that Premiere CS6 was not going to be able to read the XAVC-S files. I found that was not the case. I have no trouble working with the MP4s cased in the XAVC-S file structure. Usually i just pull the MP4s right out of the Clips folder.
One word of caution: In the past i have had trouble with the AVCHD file structure in that i was only importing the MTS files. I found in continuous run situations, where i was rolling for a few hours continously, that between each 12.5min file there was a 6-frame audio break. This happened because i removed the MTS files from their AVCHD file structure. If i would have left it intact, i would not have that problem. So i’ve been taking the same approach with the M4_Root folder–keeping the entire folder with all it’s contents for more major shoots. smaller things or short clips i just steal the MP4s out of the Clips folder.
not sure if this is totally correct, but it’s been working for me and my projects so far.