I live in Costa Rica and travel around quite a bit and have never used a travel agent. It's easy just to book directly. I would NEVER book an All-Inclusive. There are many many comfortable hotels and lodges all over Costa Rica and also lots of restaurants.
Costa Rica, unlike some other countries where AI's are popular, has a great tourist infrastructure all over the country. So no problem there. The vast majority of tourists here do NOT use an AI.
At Samara Beach, I can recommend Villas Kalimba. I know families who have stayed there and liked it very much.
This is a good place to look: www.anywherecostarica.com They have a questionnaire where you can provide your answers and they will propose an itinerary or two for you. They can arrange transportation or you can do it on your own.
The shared van shuttles are just between destinations. In a local area, you can book organized tours for your excursions or just use a taxi to get around. In many locations, you can rent a car for a day or two.
To get the best out of your trip, you will need to do some research. But when I plan a trip, I think that doing the research is a fun part of the whole thing.
If you get confused--
1. Figure out what you want to do and see
2. Find the places to do that
3. Look at the lodging available and book it.
There you go!
For a 7-day trip, I would recommend no more than 2 places. Most people like to visit a volcano/mountain location such as Arenal and then a beach location such as Samara.
There are two international airports: San Jose SJO and Liberia LIR. Where you go will depend somewhat on which airport you fly into since they are 4 hours apart.