A hotel package implies that you will stay in a hotel on one of the islands. In the mornings you will start with one of the many excursions and in the evening you return comfortably to your own hotel. The excursions, however, are limited to the inhabited islands and sometimes small islands near Santa Cruz.
You may also opt for a single overnight stay. If you are not keen on fixed itineraries or planned trips, this may be the right option for you. You can determine your own journey all by yourself.