Re: How much deck over the cabin do I remove?
You'll find plenty of threads online about how to sound out the deck with a rubber or plastic hammer (or two fingers) to find out how far the rot goes. Or you can drill a small 1/4" hole every 4" out, checkerboard style, until you come to dry wood. Don't be surprised if the wet area is much bigger than you expected.
Whether to cut from above or below is a whole other issue. If you cut from below, you have to hold the repair "UP" without getting too much epoxy in your hair while it dries. Then you can cover it with a new overhead. But if you cut from above, I'd suggest that's easier to rebuild since gravity is on your side, and you can apply a new non-skid material over the repaired area to hide the repairs. Which should be less work than installing a new overhead in the cabin.