Those are just 2D images that are mapped on a 3D model.
A 3D model is another file. Made with 3D Studio or Maya for example.
In that file you can tell which piece of the 2D skin (or texture) is to be placed where on the 3D model.
That is why a texture often is called a skin, because it wraps around a 3D model like a skin.

You should save the template as a BMP file with 256 colors and then load it into the simulator.
I assume you mean the templates you found here, so you would have to load them into IL-2: FB.
That is why testing skins sometimes is a lengthy process. Test in the game, make changes and test again...