I don't recall EVERY case, but for most cars, you may find three scenerios:
1) Cars that have a sample color applied uniformly.
2) Cars that that the color applied as a mapped texture (yes, even plain color cars).
3) Cars thave have the mapped texture inside the car model (therefore, not in the skin folder)
Quick n' dirty solutions for each scenario:
1) Open the file (commonly a file called "detail_color.dds", "metal_detail.dds") with Photoshop or similar. Paint it. Save.
ADVICE: You will need a photoshop extension to open DDS files (it was called Nvidia Tools, if I remember correctly).
2) Open the file (name changes a lot here, but usually refers to "skin") with Photoshop.
- Create a new layer on top of it.
- Paint the color parts with a blending mode enable (Darken, for instance, works in most cases) so the color adapts to the original layer below.
- Save as dds.
3) Same as above, but first you have to extract the dds texture using CM's showroom.
Well, as you can see, solution requires a slight degree of programs handling, but I hope this helps!
EDIT: I'm uploading a quick paint on a VW beetle that only has one colour. By moving the floating color layer you may find it's not even too precise (the blend layer allows me to exceed the borders in most cases). Once you have that layer finished, you may colorize it using the "Hue-Saturation" menu, and create different colors. Hope this practical example helps!
https://sharemods.com/x40atlyj2xjd/Beetle.psd.html