Hi Tracie,
The way it’s laid out, you have to drive through Quepos to get to Manuel Antonio so many people use them interchangeably because they are so close to each other. They are very different though. Quepos is a busy little port city- it’s where many of the locals live and do business. There are a lot of stores there and not too much of interest to visitors. People visiting the area usually stay in Manuel Antonio so that they’re closer to the park, beach, and all the restaurants. There are some restaurants and shops in Quepos, but the vast majority are in Manuel Antonio–along the one main road that starts in Quepos and leads to Manuel Antonio National Park–or on side roads going off that. If you look at a map, it’ll make sense. One other thing: You might notice that some places on the border of MA are technically in Quepos- anything on the road that goes from Quepos to MA are in a good location. Have a great trip!