Having read (probably too much) about visiting the Galapagos in a yacht we found the whole check-in/out procedure haphazard and talking to others somewhat idiosyncratic.  We were forced to have an agent and in the end stayed for nearly three weeks.  We were restricted to Wreck Bay on Isla San Cristobal and Puerto Ayora on Santa Cruz and did tours from each place.  As far as we can see, it is apparent that the restrictions placed on yachts in the Galapagos Islands are more about getting money than about conservation, so with that in mind I decided to trust my instincts and insisted on paying the park fees for all of us, personally, at the Charles Darwin research station.  That way we could at least be sure the funds reached the right place.  Otherwise it seems a most haphazard way of collecting fees from visiting yachts.  That all said we would not have missed this opportunity for the world.  The wildlife was unbelievable.  The fact that we could get within feet of the marine life, animals and birds without seeming to scare them was a privilege beyond dreams and apart from the bureaucracy the people we met were friendly and helpful.  But now it was time to leave on the next part of our adventure.