If I use multicolored overlays, i'll actually tape off the overlays and limb and use some flat black spray paint to keep the fibers from showing, I also have used the black sharpie idea like Kenny stated. I usually do glass, then phenolic, then glass again so the glass blends into the limb easier. I also have used smooth on to coat the overlays to "seal them" before I put finish on. That helps keep the fibers from showing as well.
Dave