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If you're using motioninjoy, and have selected Xbox360 emulation, then there's no mapping involved. As long as your controller is plugged in and enabled, then starting Reckoning will default to using your controller. This is an important point, as your keyboard/mouse will only partially work, and if you ever want to switch back, you'll have to disable your PS3 controller or unplug it completely (either by unplugging your bluetooth toggle, or if you're using a miniusb cord, unplug the controller from that).
Obviously, you'll see Xbox360 buttons on your screen as prompts, but it shouldn't take a rocket scientist to figure out what buttons they correspond to on your PS3 controller.
There's no setup needed, so I can only say you are possibly overthinking what it takes to use your PS3 controller.
For the record, I used mine, so I say the above through personal experience. I also found keyboard/mouse to be far superior except for reckoning mode and weapon switching. ;)
Also, try unplugging the controller and plugging it back in. I have to do this after the computer has been on standby. I assume because the drivers aren't initialised properly after standby is resumed.