I can't give up that easy. Covering the spots is out of the question, but thanks for the suggestions. The photos don't show how deep dark brown the deck really is. The camera flash lightened it a whole lot in the photos. A black magic marker would hardly show on this dark color.

Ok - I know you guys think I will make a mess if I sand off the glass in these spots, and I appreciate your concerns/warnings, but I am going to try anyway.

So....Here is what I may try:
1-Sand off the glass, and dings in the wood
2-Stain the wood with aniline dye to closely match color
3-Build any low (sanded wood) spots with multiple layers of un-thickened epoxy
4-Glass the spot; fill weave, and sand/blend area
5-varnish spots, then re-varnish whole deck

It looks to me like each successive step in the process will require delicate color matching/blending.
My questions to you guys:
1- are there any non opaque tints/stains for epoxy available? Something that will just lightly color the epoxy.
2- Jay, you mentioned tinting the varnish. What did you use for tinting?

Larry....