Personally I only combine colored layers depending on category (hair, skin, eyes, etc). But I also create separate layers for a part which is supposed to be a certain color so that shading with clipping layers isn’t as much of a hassle. As seen with Sephiroth’s clothing in most of my drawings, I usually color certain parts on one layer and then the rest on other layers. I also make sure that the colored parts aren’t close to one another, and once I’m certain that the shading looks good, I combine the layers of that certain color. But hey, you do you