output from factory keyless entry?

No, all the window module requires is a single pulse from the LOCK wire and it will roll up the windows. Any KE, alarm or remote starter can do this with the window roll up module.

OH, I got you now... ok...

Do most people put them on the window roll up vs down?? I thought it would make more sence to make them down so that you can air the car out before you get there??  (which would still need the seperate one so that it doesn't roll down each time you unlock the car (aka rain)...

if I use the door lock for the trigger, would that mean that everytime I lock the car, the windows would roll up on me too?

What you need i a channel expander connected to your  door lock wire

http://www.autotechs.com/items/item237.htm