I used the following to get the buttons to work right:
Alias {90,91,88,89,41,40,32,33,73,72,48,49,3,2,1,0,4,6,1 0,5,7,11,9,8}
The important section that you need to be aware of is:
3,2,1,0,4,6,10,5,7,11,9,8
I tried changing only only one instance of Alias but that didn't work so I just modified all instances.
I also found that you can pair the controller up through bluetooth by putting the controller into pairing mode by pressing Share+PS and you'll see the controller light begin to strobe. A word of caution though the controller does not turn off after a couple of minutes of being idle. You have to manually turn it off by pressing and holding the PS button till the light turns off.
Here's the neogaf thread where I found the FFXIV.cfg info:
http://www.neogaf.com/forum/showthre...703501&page=13