Sorry for the language but... Oh gosh this could be a thing. Jasper could become a corrupted gem...<<< haha, you were spot on buddy
LittleBig Pearl, by Amber Figueroa
I don't even know anymore xD | Sapphire & Ruby from Steven Universe
The easiest way is to lock the lineart layer (so, yes, that means that it should be separate) and use a soft brush (any kind will do) to colour delicately over the lines.
How I color clothes by Yamicchi.deviantart.com on @deviantART