It's one of the things that was bugging me; was thinking of how to do it. My personal suggestion would be to paint the ships entirely in original colours first, (metals too, colour scheme etc) and then add the growths on top in their respective colours. At the moment, the ships just look like... well, blobs. There's no real definition, which is a shame as the detail is actually really good. I'd also recommend things like gun barrels maintain their metal colours if they're still guns.