Hi Chief. My walkthrough might help.
http://www.simviation.com/lair/Repaint2002.htmThere is no limit to the number of variations for a particular aircraft. The new Texture folder can have any name you wish providing it follows the FS folder naming conventions. Texture.3, Texture green, Texture.CAP etc. The suffix following the period will be defined by the texture= line in the new Aircraft.cfg entry.
Repaints usually come with a sample Aircraft.cfg entry. Paste that into the CFG instead of creating your own as in my example. Make sure the new [fltsim.x] header is numbered in sequence or it won't work.