RJP probably has the best answer. The Aggressor does a great job of coordinating the flights to/from the islands, meeting the passengers at the airport in Quito or Guayaquil, doing a group check-in to avoid individual excess baggage fees, and then picking up the passengers at whichever Galapagos airport is being used and driving them to the boat. Adding an extra day or two in mainland Ecuador before the trip is a good idea in case there are any luggage delays.
On the last day of the trip, the Aggressor will dock in Puerto Ayora, where passengers can roam the town and have dinner. P.A. is a nice little town, with hotels and restaurants of all sorts. Logistically, it's probably much easier to book a few days in P.A. after the trip, when you can simply move yourself from boat to hotel on the last night of the liveaboard, then get your own flight back to the mainland and then back home.
In either case, contact the local Aggressor office in Ecuador for the best advice, as they coordinate the hotel overnights on the mainland and the island flights and could probably assist you with staying in the islands before or after the trip. If you let them coordinate things, you won't be left behind if something goes wrong.
