How, if possible, might I make it so a part cannot be heavily effected by the paint on a ship, or so that a decal isn't affected by the value or color wheel.
Gray use a different layer.
If you look on the left, there is a row of fades. the one in the middle is what it is supposed to look like. How can Fix this?
Lafiel use a different layer.
This, but use the roof_doodads or roof_turrets layer as they're above the roofs layer. Don't use the roof_windows layer as that's disappearing in the full version.
roof_doodads
roof_turrets
roofs
roof_windows