Steve. I haven't tried FS Repaint. I assume this is for FS2002 or FS2004. The method I use for repainting the old way should work just as well for you. Before starting work, take a copy of the Texture folder of the aircraft. Right-click on the Texture folder & select Copy. Then right-click anywhere in the folder & select Paste. You will now have a new folder alongside the original named Copy of Texture. Rename this folder using the FS folder naming conventions - Texture.3, Texture.green, Texture.myrepaint, whatever - & edit Aircraft.cfg to recognise it as a new variation of the aircraft. Now you can start repainting it.

Before you start repainting, you need to right click on the plane you want to edit, in the box on the left, and select "new variation".