You would have to create the variant first (say you call it RPT1), then replace the copied textures in the texture.RPT1 folder with the paintkit textures.

Example - I'll load up the default Learjet and create a new variant, and just call it variant "2".

FS Repaint will create the texture.2 folder and the appropriate entries in the aircraft.cfg file ([fltsim.2]) AND create a copy of the textures in the texture.2 folder.

Assuming you have a blank paintkit (for which the textures have the same names) for the default Lear, you will copy your paintkit textures TO the texture.2 folder, overwriting the FS Repaint copied textures.

When you open FS Repaint again, and select your new variant, you'll see the default Lear with the blank paintkit.