Everyone staying at a Disney resort is entitled to a round-trip on Magical Express from the airport and back again, regardless of whether they actually fly into the airport or not.
Your best option is to call Magical Express directly (866-599-0951) and tell them what you're doing and what time you plan on dropping the car off and taking the bus. They'll enter you in the system without assigning specific flight info.
It's best to call DME directly rather than trying the main WDW reservations line, since I've found that a number of central reservations CM's typically have trouble dealing with out-of-the-ordinary DME situations like this. There also doesn't appear to be a way of scheduling this information in the online DME info page.
You'll get the yellow luggage tags in the mail, but you can just throw them out since you'll have no use for them.
Lastly, depending on your rental agency you could always look into dropping the rental off on Disney property and avoid DME altogether. The Alamo and National location at the Car Care Center near the MK parking lot have a van that can drop you off anywhere on property, as well as a desk at the Dolphin that's within walking distance of Epcot and the Epcot resorts. Most other major rental companies have desks at the hotels on Hotel Plaza Blvd, though shuttle options vary by company.
-Rob