Your tour operator will try to sell you larger side trips for substantially more. Some are well worth the price. The trip to Havana is a must. If you can then get it with the night club visit. Jungle trip is OK and is an opportunity to visit Varadero beach where most of the tourists go.
Car rental is available at the resort but is rather expensive.
Now that I know the lay of the land I would rent a car rather than taking the tours. Suprisingly few people went in the water. It was cool but just fine for snorkeling without wet suit. Best spot is directly out from the beach bar. We brought our own gear, but loaners are available at no charge.