Nevermind Einar helped me with my problem in a email. If anybody needs help here it is.
Pull batteries
Put batteries in
Hold down sync while powering up controller (you can do this before plugging in the PnC cable)
Wait for LED3/LED4 to turn off
You can stop holding sync, and plug in PnC cable to computer then to 360 controller
LED's might turn off that's o.k., just launch the hidbootloader.exe and go from there