I am working on sanding and finishing my CLC. I was hand sanding around the combing and I went through to the wood. Do I need to re-coat these thin areas with epoxy or can I just count on the Varnish to protect those areas?

Also when sanding the surface some areas have kind of a spotted checkered pattern, what is this? Am I scratching the glass(Is it OK to cut into the glass?) or have I just not sanded it all the way smooth in those areas? When I wet it with water it looks fine.

Thanks in advance. CHad