Getting out to the islands can be a little tricky, and it may appear as though the only means is an organized tour that costs way more than you ever planned on. However, it can be easier than you think once you get away from all the tourist services and naïve backpackers with access to unlimited funds.
Leaving from Panama City, the road to the Caribbean coast is monopolized by transportation services – you must take an SUV to get out there and the cost is $30 USD each way. You can get a reservation through your hostel, leaving around 5:30am. Once you get out to the boats it is not too difficult to hop on one and decide where you want to go. You will need to pay a $2USD fee at the dock, they will give you a token (a poker chip or a small piece of paper) which you will need to hold on to until you return, if you lose it you will have to pay the fee again when you make it back to the mainland. It is usually around $10USD to get out to the islands and once you get to the coast, you can spend as much time as you want island hopping, taking rides on passing boats and experiencing as many of the 365 islands that make up San Blas as you can. (NOTE: Sunedup is the main destination for the backpacking crowd)
Getting back to the dock is fairly easy, you can organize a ride from wherever you are staying and once you make it back to land, you will find plenty of SUVs lined up corralling people to take back to the city. Again, you will have to pay 30USD to make it back.