Honestly I think the split stay will be fine. As long as you understand you might be out of a room in between, it's really not too bad. Personally I do find them a tad bit annoying when it comes to packing stuff up to switch rooms, but the benefits of them outweigh the negatives, especially in this case. WL and YC are my two favorites on property and they both provide unique experiences and benefits. WL is great for MK access while not being as pricey as monorail resorts, and YC is amazing for HS and Epcot for sure, but the boardwalk area can't be beat. At Christmas, both resorts are beautifully decorated and offer convenience that is unique to their areas. I'd say just make some plans to kill the time it might take in between getting your new rooms (i.e. going to the park, a sit down lunch, Disney springs, etc.), and don't really rush yourself when it comes to checking out and moving to your next room.