They realize the only way to get back in their own bodies is to understand and accept their current body and all of it's problems such as college, family and friends. They both work together as a team to get as far as they possibly can in each other's lives to set each other up for a great future and hopefully for great careers.
While spending so much time together and learning everything that each other's knows, the best they can, they start to truly respect each other and decide to make the other person's dream's their own dreams. Woody wants everything Nell want's and Nell wants everything Woody wants. If their future ends up being each other's, they want to honor that as a respect for one another.
Nell takes intense training from Woody to learn everything she can in Woody's body to help him get his football scholarship. Woody learns everything he needs to know to land Nell a spot into Yale. They both realize the little details about each other that matter and learn each other's hearts. They start developing feelings for each other. They learn why they were always in fights and it wasn't because they didn't like each other but because their families couldn't get along. Their families finally accept them as friends and possibly more.