Well, after downloading both Paint.net and the paint kit you mentioned, I'm a bit stumped. How did you open the files in the first place? Paint.net is incapable of opening that type of file. Or at least it is without some kind of upgrade or plugin.
At any rate, this seems to be your issue. If you're going to paint aircraft, the only answer is to get a good repaint program. PSP or PhotoShop are fairly expensive (PSP ~ $100 US, PhotoShop ~ $700 US), but there are other options out there. One of which is a dedicated program designed for FS. It reads the FS model as well as the textures and renders a 3D image of the texture on the model itself, so you can see exactly what the changes you are making can do for the model. It is called
FS Repaint and is only $30 US. Cheaper by far, and powerful enough for what you want to do.