You should use the latest version of Motioninjoy (
http://www.motioninjoy.com/blog/motioninjoy-ver-060004-available) and combine it with the offline files of v0.60003 which I posted earlier in this thread so you aren't dependent on their website being up (it went down last week causing problems for most users because the offline wouldn't work). Then, follow these instructions which are hopefully accurate as this is what I did:
-Open up DS3 Tool
-Select Custom and click on Create
-Click on Default
-Click Save
-Click on the existing custom profile (MotioninJoy Demo Profile or some such)
-Click Delete
-Click Save and give the profile a name
-Enable the profile
If necessary - and it was for me - download the GamePad Fix tool (search via Google) and set up the controls for FIFA 11 and then copy the "buttonDadaSetup.ini from My Documents\FIFA 11 to My Documents\FIFA 12 and if you're paranoid, make it read only.
Motion sensors probably don't work as it acts like a PS2 controller but I'm not concerned with that. Analog sticks work perfectly fine - just be sure to load DS3 Tool when you restart your computer and enable your custom-made profile before you plan to play or half the buttons won't work.