I haven't read all the posts on this thread, so pardon if there is some duplication here. I think your plan (EP/MK) sounds like so much fun! We (DH, DS, DDIL, and 2 grandsons now 6 and 9) have been doing 10 or 11 day split stays (with a side trip to Universal) for at least our last 3 or 4 trips and we only get to go every 2 or 3 years so I think we started before the younger boy was even born, but we love it.
I pack knowing we will be moving and I never unpack things I wont be using till our 2nd resort, so packing to move mostly involves throwing dirty clothes in a bag and takes no time. We check our luggage in in the morning to be moved and head to our first park usually right at opening, and later return to our new room. Being able to check in on the app means we don't have to go to our new resort until our room is ready.
The heaviest burden falls on DDIL, who does most of the packing for the boys- but she is a great traveler so all goes smoothly. The boys have had a stroller, so DDIL might bring a few extra things they might need before we have a room, and the boys are good to go. They can even nap in the stroller and have.
(Our splits have been at AKV and BCV - the boys LOVE seeing all the animals right outside their balcony and outside the windows as we walk down the hall - and I LOVE having my morning coffee with the giraffes right outside - but I have often thought that while they are young and love MK so much it would be fun to stay at the Poly once - even though the building and remodel have taken away some of the charm. Is the construction finished? (I feel like GF might be too stuffy for our exuberant boys.)
On our final check-out day, we love to spend what time we have at Storm-Along Bay - BEST hotel pool ever! - so we always start at AKV and end at BCV, though since I expect your boys will love being near MK more than Epcot I might do MK 2nd. The sand bottom pool is so perfect for little ones.
We were afraid with the split stay we might not get all the ADRs we wanted, but DDIL kept at it in the wee hours of the morning and got everything - even the hippo experience at AK this last trip.
Whatever you do, I know you will have so much fun! You get to see the park though your boys' eyes, which is a whole new kind of wonderful (which we are now getting to experience with my grandsons)