I believe that it's covered in the manual that came with it.

You go into the sim, select to edit the model you want your paintjob on, the "export" it. The sim will then setup a .tga file with that model in it's game paintjob in the .tga file. You simply pull that file into your paint program and paint over the game paint. When you file it back, it'll be setup in the sim for you to choose.

I've painted a Sukhoi and an Ultimate that match the ARFs I'm flying. It's magic. My models fly a bit different in real life than they do in the sim, so I tweaked them in the sim to match up. It's even more magic now.