I would recommend that you put all of the food, drinks, and food enrichment items inside (or outside) and then put all of the toys and items that don't need keeper attention outside (or inside). This could work either way. This is so you can have a smaller, more realistic looking door that just your animals can fit through, and not the keepers. The only thing would be the cleanliness with the poop, but I think you can turn that off in settings (Sandbox mode at least).
Or, another option, which is what I do, is to make a indoor and outdoor habitat seperated from each other. The game thinks it's two habitats, which it is, but you can still make the illusion that it's two, if that makes any sense. So in "the winter" I'll close off my outdoor exhibit for my Tapirs, for example, and move them into their indoor exhibit. Then in the spring or whatever, I'll have it be one big exhibit (with what I mentioned before) or two seperate exhibits with two seperate groups of animals.
Hope this made any sense, because while it may make sense in my brain, it may not in yours! But yeah, I would definitely try to use indoor/outdoor exhibits honestly as much as possible with as many animals as it makes sense to, because it is a really realistic part of zoos, especially in temperate regions, like where I'm building my zoo.