Is it possible to cover up the windows and paint ontop of them? like, if i cover up a window and paint over it the window wont still stay white when covered.

I didn't get this model on the $9.99 sale yesterday as I have enough 737s to paint! 

Typically, all you have to do is modify the alpha channel to blank out the windows.  This is pretty standard on most models, regardless of developer, and while I cant say for sure on this one, I see no reason why you could not blank out windows in the same fashion.

I did the same on this pax model that had no freighter version...


I even altered the bump map slightly to raise the lip of the cargo door very slightly and you can see the light catching it on this pic.