The problem with that is if a area of the ship is red it turns purple, believe me i used to uses that same technique.
May be better ways of doing it, but one way you can avoid that is using raster layers.
In PSP9, I will add a raster layer, then select the background layer and clone only the sections I want to edit on that raster layer. That way you can change hue, color, transparency or anything just on that selected layer. Repeat the same thing on other layers for different parts as many as you want, and it won't effect the base picture. then when your done, merge it all together. Works great on any project, not just re-textures.