I too have had this problem, I found the best option was as follows,
Dont connect stick at first.
Start PS3, assign game pad to controller 2
Start game goto options, controls, layouts, pc stick
Connect joystick
Hold ps3 button and turn off controller 2
now using joystick, goto custom layouts and assign buttons.....however this does take trial and error to work out which buttons on the joystick relate to the triangle button so you can make the changes
Or thats how I think. I did it.... this is from memory
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