Stress cracks and filling holes

[Yamtt125]

Fellow:
There is lamination left in the holes on the console, but i'm not sure about the holes that were drilled for the rub rail....some of them are pretty bad. I'm also thinking about adding something to the top of the console so i can flush mount the electronics. If I did this, i would also put another layer or two of new glass all around the console...especially the bottom because that area is weaker. Do I still need to fill the wholes, and fix the cracks if i plan to glass the whole thing again?
-Andrew