Youre welcome!
1.) Once you have the MotioninJoy drivers working, you run Better DS3. Then you can use Better DS3 to assign your controller mappings, and pair bluetooth controllers. You shouldnt uninstall MotioninJoy, but once you have the drivers installed you dont need to use DS3_Tool anymore. Better DS3 doesnt need to be installed, just copy it to your computer somewhere and run it. If you want it to start automatically with windows, just drag a shortcut of Better DS3 to your Startup folder.
2.) No, currently the drivers cant be loaded and unloaded with Better DS3, sorry.