The easist and quickest was to get around is by cab and it's worth getting friendly with a trustworthy taxi driver who will pick you up and take you around the island.
We met a very reliable Taxi driver in Stone Town who charges reasonable prices (cheaper than they will quote you in the resorts). From Stone Town to Paje we paid $45 and took about an hour. From Paje to Nungwe it will be about $60-70 which seems a lot but the resort were quoting $100!
His name is Hery. He is also a tour guide but we didn't take him up on his offers. His number is 255-777-469721
To get to Paje from Stonetown, arrange a taxi from your hotel. It should cost no more than 5000 Tanzania Shillings, but you can get it for less. They will pick you up in a mini van and take you to all the good guest houses. You choose which one you like. They are very accomodating (to Paje anyway it was a bit frustrating going to Kendwa).