Hi Elaina,
My family loves Disney's Animal Kingdom Villas. The atmosphere is amazing and exotic. The Villas are beautiful, and the bathrooms are hard to believe. Your kids will love the zero entry pool and Kidani Village has a water play area. To be able to see animals from the resort is something my children love and will get up early to see.
I find that splitting resorts works if you have at least three days at each different resort. It will give you a different feel to your vacation, almost as if you have two separate vacations in one trip. You will need to be in the room for your luggage to be picked up and then it will be transported to your new resort and left at the front desk area. You will need to pick it up when you arrive at your new resort.
The Villas at Wilderness Lodge are wonderful as well. You feel that you are actually at Yellowstone National Park, complete with geysers. The Cabins at Fort Wilderness would be a great fit for your family. Your kids will love being in their own cabin and have adventures all around the campground. I am not sure which one you were thinking of doing but each would be fantastic!
Please send me a follow up question if you have any other questions, Elaina. I hope you have a magical vacation!