Just as a thought, but I have found a way that worked for me, with eyes at least. I found that if you make the piece you want to remain a certain color its own image it will remain its color and not go to a different color. For example, I made eyes with pink eye shadow. Unfortunately you can't change the eye shadow from pink, but at least it won't change color. The layer/image for the eyeshadow I named _c3 while the iris was _c1 and the actual eyeball and lashes were _c2. Because the pink was _c3 it was lower than the other ones, but as long as I was careful it still looks fine. It basically works in layers. So if you were going to make a few orange scales or something you could either name the scale image _c1 so they'll be at the top or poke holes in the skin and have the orange underneath as _c2.
I don't know if I made a lick of sense but I hope I did. Basically what I've gathered from looking at the gen files is that the _p1 part controls the order it's in and all associated pieces must match, while _c1 controls the layer numbering which it's presented in. 1 would equal top of the layer pile. I think the _m001 controls the colors it uses but from my testing eyes still use the eye gradient even if you change the number to the hair gradient. So maybe I'm wrong.
If this seems rushed it's because my brother is dragging me away to play a game. Love the work! Keep it up!
I was doing exactly this thing at the female eyes,I made some custom scales,and it looks beautiful,for now I will improve it more,and post it here,maybe later if I finish it

Thank you,and yes,I will be careful,the results must be great.
Update:I made a few mess with my resources,and it doesnt work at the eyes part to have more than 2 layers,for example I thought I can make scale part as a Main color,and Eyeball a Sub color into generator,so we could have dragon scales green for example and eye color blue.
What I could make until now it is that if I change the eye color,into generator,it change the scale color too,so they both will be blue,depend what color of the eyes you choose.So only 2 layer I can have there,the same restriction as the dragon horns and ears that
@Tuomo L asked me about.
But it looking very beautiful this way too,so keep in touch and check later my updates that I will put in.Have a nice day ^^
@Derex000
BTW I think I could put the scales,as a face mark and that way we certainly will have a different scale color,so I will check and we will see what It will be my final result
