How to program a CAN-BUS Arduino shield to control car windows?
What model car do you have?  Most cars do not have the ability to control power windows from the car computer.  Late model cars will have the ability to control the window motors using bidirectional functions on a scan tool.  On any car, the window motors have two wires, if one wire is given power and one ground it will spin if you switch the wire that gets power with the wire that gets ground it spin in the opposite direction.  In my experience the way power windows work are both wires are ground while the switch is in the neutral position and by flipping the switch the switch will disconnect one of the grounds and replace it with a power.  Find a wiring diagram for your car, and look at how the windows are controlled.

Get a 2 relay breakout board such as this one (make sure you check the current ratings):
http://www.amazon.com/SainSmart-2-CH-2-Channel-Relay-Module/dp/B0057OC6D8/ref=sr_1_1?ie=UTF8&amp;qid=1400730995&amp;sr=8-1&amp;keywords=arduino+relay+12v

Connect the ground wire to the normally closed (when no power is applied to the relay this is connected to the output wire) side of both relays and the 12v power to the normally open (when power is applied to the relay this is connected to the output wire)side of both relays.

In order to control the relay breakout board you choose one io pin per relay and set it as an output, then connect those pins to the corresponding pin on the breakout board. Set one of the pins to high (you apply power to one relay) the motor now has a power and a ground connection, set the opposite pin high to spin the other way.

I would place this in the driver side door underneath the window master switches because you can have access to every windows wires as they come out of the master switch.

Some late model cars will have a different set up than the one described, but the window motor will only have two wires (it is just a brushed DC motor) just find the window motor and hookup there.

I hope this helps.