keep the deck as low as possible to maintain a low center of gravity. you should also base your decision on your experience/skill. if you and your fishing buddies are boat savvy and have good balance, then go ahead and deck it.
i suggest you don't make the deck permanent until you have tried standing on it in the water. if you feel it's too tippy, adjust accordingly. when you find comfortable height, that's the time to add the carpets, compartments, etc...