Obviously, I will have to sand alot but how do I know when to stop sanding.
Pictures would help with a diagnosis.
If you choose to sand, use 60 grit and stop when the cloudiness is gone before you hit fiberglass cloth. Then I would add two new coats and sand with 120 then 220 and varnish.
If you think you need to add new glass then removing the old glass would be in order.
Start removing glass on the hull bottom. Go slow and get the feel for lifting the glass without pulling up wood with it. If you can remove only the glass and leave the epoxy coating on the wood, you won't have to sand to remove ALL the epoxy down to bare wood. If you can leave the wood epoxy coated then you can sand the surface lightly with 80 grit to smooth it and then glass over with good results.
Starting glass removal on the hull bottom will give the experience to see if you can do the above and make your deck come out well.
All the best,
I hear and I forget. I see and I remember. I do and I understand.