Just change the tga file thats in your data folder (ex. DataMod1) and then it will only be modded for that specific mod map.
As for your problem with painting the storm trooper red, I suggest you use photoshop when editting ai skins, which are typically more detailed than unit skins. Working with shading is the main prob with paint (unless your a really good artist with paint that is), but to do what you want to do you need to get photoshop or at least something like it off of searching on google. But painting it a solid red color might be noticeable if you were planning to do a dark level in which shading does not necissarily matter.
Good Luck with your Hypori Mod