We fly into the San Jose airport which is actually located in Alajuela. We stay overnight at a wonderful B&B, Pura Vida Hotel. Sometimes we rent a car in Alajuela and drive to Quepos, other times we have used the resort's shuttle and rented a car for some time in Quepos in order to go to the places we want to see before we just hang out at the resort.
Most of the tours and activities will pick you up and drop you off at the resort. The resort also has a groceries shuttle that leaves at 11 the morning after check-in so you can stock up for the week. Taxis are quite inexpensive.