Since you are leaving a Disney-owned resort to fly home on JetBlue, you can use the Resort Airline Counter at your hotel to check your luggage and check in for your flight even though you are not using Magical Express to get back to the airport. Counter opens at 5:30 AM, you need to check in at least three hours in advance of your flight, all members of your party must be there - it's just like checking in at the airport, except ideally the line's shorter. Your luggage will be transported from that counter to the airport, then onto the plane and to your home airport, without you having to touch it. You'll be given your boarding passes; once you return the car, you enter the terminal, take the escalator up to Departures, and head directly to the Security lines. Simple.