I did power windows and locks in my '06 DC. Can't remember EXACTLY where I caught the wires, but I know for the drivers door I had to go into the door itself, and basically caught the wires at the motor.
For the passenger window you have two options... if you're a generous owner and want both the driver and passenger to have one-touch operation (assuming your Window Control Module (WCM) has the capability, and most do), then you have to run wires to the passenger window motor. If you're not so generous, you can catch the wires in the drivers kick panel or in the door itself coming out of the window switch module there. I was generous and ran to the passenger door motor
For the rear windows, since really the only person back there is my daughter, and she would view it as a toy, I caught both rear windows in the kick panel.
Also of note, having installed for quite a few years, I strongly urge anyone doing this not to be lazy and put the WCM inside the door
!! Putting a piece of electronics inside an environment that is prone to moisture that doesn't claim to be waterproof is not a good idea... put the WCM in the cab where it will stay much drier. I only had to run 4 wires into each of the doors, and the grounding options inside the door aren't that great.