Normally I tell people to do the value first then the deluxe, it's really hard to leave them. But since you are already booked, possibly ask for a renovated room at Pop. They look to be pretty decent.
I do split stays just about every trip. I always call down the morning we are transferring and check out then even though I have done on line check in, unless I get the room is ready text, I physically go to the front desk of resort #2 and check in. We do the transfer very early in the morning because I'm an early riser, we are normally at resort #2 by around 8 am. You can get your bags transferred by Disney. If you have a car this isn't necessary, if you don't have a car you are going to either have to bus/walk to a park then bus to Pop or Uber it. You don't have to go to Pop first, you can just head out to a park, we do it because we have the car and it's too early to go to a park. If you aren't driving, try packing cubes. Pack your stuff for the first stay in designated cubes, just pull those out and either live out of them or unpack (I'm an unpacker, my son lives out of the suitcase) and then repack the dirty stuff back in them, and just pull out the cubes for the next stay. Makes it a little easier, since we drive I actually pack two suitcases. If you store your stuff at bell services or have them transferred, you have to call down to get them once you are physically in your room, they will not bring them up until you are in your room. You can also just stop by and get them yourself.
You will get the option to personalize two MBs, it isn't necessary unless you just want two, you can decline one of them.
Enjoy BC, YC is our favorite resort but we love all the Epcot resorts, and even stay at Swan/Dolphin if they are less. I agree to plan your Epcot/HS days while you are at BC, the walking/boating between them are great.