Same, lol. Actually, I don't even have separate layers for skin/eyes/clothes anymore: character flats go all on the same layer and character shading goes all on another layer set on multiply :'D I work in Procreate and I need my files to be as light as possible in order to quickly upload them to GoogleDrive and then open them in Photoshop for further editing, so I try to use the least amount of layers possible. The only things that go on separate layers are panel backgrounds... but then they also get merged into a single layer XD
The way I usually do it is: select color from one of my saved palettes > use it to color ALL recurring objects in that color on each panel > move on to another color > proceed until I've got all the character flats done > select character flats, create a new layer, create a mask out of selection and set the layer on "multiply" to do the shading.