Maybe you could brush on the color and then wipe off the excess with a paper towel.
I was going to cover in grey fondant. Do you think I should cover in a different color?
I would cover the whole thing with gray, then line the windows with a dark grey to give them depth....as far as shadowing, I use a type of sponge method with mine to get a look that I want. I take a coffee filter or paper towel and ball it up so that I have one flat side to use, then lightly dip it in my color or brush on just a little and sponge it on. I would go light, because you can always put on layers to make it darker if need be! That is what I have done!