Pull Pull Pass Through. How do u do it?
Those holes are easy to fix. Cut them bigger so they make a nice rectangle shape. Then cut pieces to fit. Before you glue them in, put the holes in them for the nyrod or whatever guides you are using. It will look fine after you glue them in place and sand it a little.
If it's already covered, just remove a patch of covering and tape over it to protect it from the sandpaper.