I always mask off my motor if it's on the plane when I paint, but there's no harm in just painting right over the skewers, servos, control arms, pushrods, and everything.
I have not used it, but there's a material called "frisket paper." It's a low-tack vinyl type material, a lot like transfer tape, which can be used to make masks for spraying different patterns. Cut the frisket paper into whatever stencil you need and apply. It doesn't stick much so it should be safe for masking over other dry paint.