You have a couple of choices. I preferred to walk barefoot on the boat and have shoes that are good for walking on rocks, sand and in the water and leave them in the storage area in the back of the boat when I board. You cannot wear the off-boat shoes on board (because of the sand). I like Tevas or something similar for walking around on the islands. Make sure they are good for rocks, though - there are a lot of rocks on the islands. Have a wonderful time! I did!
The upper deck has full windows and great views, but even relatively calm seas can produce significant rocking motions. The lower deck is a bit calmer, but noisier because of the engine noise and you don't get a window at all. If you can stand the increased rocking, and if you secure your camera and other breakable things, I'd choose the upper deck.