Say your repaint was all blue........make a folder named:

texture.blue and put all the contents in there

Now open the aircraft.cfg file and make a new entry in it.
Taking the example of the Cessna:

[fltsim.3]
title=Cessna Skylane 182S Paint3
sim=Cessna182S
model=
panel=
sound=
texture=3
kb_checklists=Cessna182S_check
kb_reference=Cessna182S_ref
atc_id=N700MS
ui_manufacturer=Cessna
ui_type=C182S Skylane
ui_variation=White with blue and purple
description=When Cessna saw how well their Model 180 was selling, they looked for a way to make it an even bigger success\s the answer was the Model 182.  The Cessna 182 Skylane feels and acts like a heavier, more powerful version of its sibling, the 172 Skyhawk.  The airplane is a workhorse and a stable platform for flying on instruments. Even with a full tank, the 182 carries a family-size useful load and performs admirably as an aerial sport utility vehicle.

[Fltsim.3] is the last number in my file. For a new texture make it [fltsim.4]

Leave everything else alone EXCEPT the part that says:

texture=

change that part to texture=blue

Again, I used the cessna as an example. Whichever aircraft you are using use that.

PS: You can change the description to fit your desire. and the:

ui_variation=White with blue and purple

To blue only or whatever you want.

Good one AstroGeek. May I point out that to avoid conflicts it would be best to change the title= name. My little walkthrough should give you the basics.
http://www.simviation.com/lair/Repaint2002.htm

As AstroGeek says, use any name for your new texture folder providing it's different to the others & follows the standard naming conventions. Texture.4, Texture.blue etc.