Here is some FAQ's that I found from touring plans site that may help.
Members of my party are flying to Orlando on several flights arriving at different times. Can we use Magical Express?
Yes. Make sure their names are on your room reservation and that you give ME their flight information. There’s no need for you to travel all together. Each person can take a bus independently upon arrival.
I’m arriving in Orlando several days before my Disney room reservation starts. We’re renting a car and going to the beach. After I return the car back at the airport, can I take Magical Express to my resort?
This one is tricky. The short answer is probably yes. Here comes the long answer …
The Magical Express paperwork states, “Complimentary transportation services provided by Disney’s Magical Express are associated with a Walt Disney World room reservation and include a one way ground transfer between the Orlando International Airport and your Disney hotel on the day that you check in and a one-way ground transfer from your Disney hotel to the Orlando International Airport on the day you check out.” You’ll note that there is no language here about a need to FLY to the Airport. As long as you’re going to your resort on your check-in day, then it really doesn’t matter how you got to the airport itself.
However, Magical Express does want to know approximately what time you’ll need transportation, so they can make sure to have enough buses available. The only real mechanism they have to note is is via a flight number. Since you’re driving to the airport, you won’t have a flight number. This may fluster some ME reservationists. A good workaround is to find a flight that arrives at approximately the time you want to go to your hotel. Simply give that flight number to the reservationist as a placeholder.
Any other workarounds?
Well, you could just show up at the Magical Express desk and ask for a ride. I’ve done this myself twice. As long as you have a valid Disney resort reservation number and there’s room on the bus, they’ll transport you.
Members of my party are arriving on different days. Can they be accommodated on Magical Express?
Probably, just call ME and let them know what you need. I’ve had WDW trips several times where my husband either arrived a few days after me or left a few days before me (pesky business meetings). In every case, ME had no problem putting him on a bus.