Ok, when you use the controller, the USB cable needs to be connected to the PC and PS3 controller the whole time (unless you're using bluetooth).
1 After installing the software and allowing all the drivers to install, connect the controller to the PC via USB.
2 Open the "DS3 Tool" Motioninjoy software.
3 Go to the "Driver" page. You should see 1 entry in the list with an X on the right side. Highlight the entry and select the Load Driver button.
4 After it completes installing, as indicated at the very bottom of the window, move to the "Profiles" tab.
5 At the top where it lists "Connected game controller(s):" is should say something like Playstation 3 USB. If it does not, restart your computer and re-open the program to this same spot.
6 On the Profiles page, select the Xbox 360 Controller Emulator, then select the Enable button. After doing this, your computer will install another driver. Let it finish. You may need to restart after the driver finishes installing.
7 After rebooting again (if necessary), your controller should work with any game that supports Xbox 360 controllers.
**** Keep in mind, every time you reboot your computer, you will need to enable the "Xbox 360 emulator mode" since it seems to forget which mode you want every time you restart your computer.