The islands are controlled very strictly and there very limited places to stay. Santa Cruz is the only island I know of that has accomodations. The main island you would fly into is Baltra. The
Galapagos Islands are a unique place in that there's not many places I'd say its best to get a package but this is one of them.
Find a tour operator that has what your looking for and book it. It will include a flight from
Quito,
Cuenca, or Guayaquil. Accomodations aboard a yacht, boat, cruiseship, meals and a knowledgable tourguide. Then it juse a matter to determining what you would like to see and how many islands. I've been to several islands and even went diving and its amazing.
Let me know if you have any further questions.