I assume you mean that you will be dropping off the car in Puerto Jimenez and flying back to San Jose via a small plane. There are only a couple rental car companies located in Puerto Jimenez, Alamo and Solid (Alamo is also in Golfito). Usually, as is with any rental car company, there will be an additional fee for dropping the car off at a location other than the one you picked it up at. We have found that sometimes it is less expensive to use our discount through Adobe Rent a Car and drop off the car in Manuel Antonio, then shuttle down to the south. You will just have to compare prices to see what works best. If you need another quote for a shuttle van, let us know too, we know a local driver that might be able to do it for a better price.
If you do end up driving, the roads are all in pretty good shape. You could make a stop at a beach called Playa Ventanas in Ojochal. This is a cool beach that has some caves on one end that you can explore at low tide. It’s right off the highway and is marked with a small sign, just make sure to keep a watch on your car since you will have all your bags with you.
Answer for Roads from Manuel Antonio to Puerto Jimenez