All you really have to do is make sure they get enough food, water, rest, and battling experience. If you stick to a town, they've got Pokémon Centers full of nurses who specialize in keeping them in top shape, and you can probably scrounge up food pretty easily on the routes... or just let them hunt, I guess.

The thing with Pokémon is that they're really resilient, and you don't have to keep them out at all times, thanks to the Pokéballs.