Actually, in case you mean the thing that is done in Agama's Swamps, or more visibly in my Glowee, it's absolutely non-haxish. The effect however doesn't depend on the level, but on the tileset. Just replace the palette entries used by JJ2 with your colors of choice.

Another thing you can mean is use of the JJM script thingie. Not sure if player's colors change would work in SP, but at least a palette change should.

If you won't specify what kind of a change do you mean, it's really hard to help you. Do you even know anyone who's using custom colors in SP? Maybe would be smarter to ask him instead. And if you don't, wonder why do you even ask.