They would be two separate reservations. They would get bands and be able to be picked up at MCO. You set up the bands under that reservation and you can set up a pick-up for the Magical Express as well. Not everyone in a party has to come together, so just give MS the travel info and they will set up the Magical Express for your other family members.
You'd also get a second set of bands and would have to find your own way over to the 2BR. You could have Bell Services move your luggage for you, just have them take it the morning of check-out from the studio and tell them what resort you are moving it to and they will take it over for you. You'd then have to pick it up at the destination.