I have always done it from the outside. I use Krylon Ultra Flat black. I mask both sides of the windows and shoot the entire body. This way if the outside scratches the inside is black and you don't see the scratch, or at least it is not very noticable. Or you can paint the inside silver, that way a scratch looks like it is scratched in to raw metal. You will be amazed though how well the Krylon ultra flat black adheres to lexan, and does not flake off like other spray paint does. I have done no less than 5 bodies like this, and it holds up as good or better than lexan paint. Slowngreen will verify this as well. He has painted quite a few bodies using this method, with one being a slash lid most recently.
I have also used Krylon ultra flat olive drab on my CJ8 crawler body, and it worked great as well.
One nice thing about using this method, when it starts looking a little beat up you just remask the windows and throw a fresh coat on, and it will look new again.