I booked on Expedia several times. Once the reservation is booked, you will need to call Expedia and ask them to get the Disney confirmation number for you. When you have that, you can link your reservation in MDE and it will appear just as if you booked directly through Disney. If you choose to purchase your tickets through Expedia as well, those can be linked to your MDE account as well.
The Magicbands will be processed exactly the same as if you booked the trip through Disney. You will go into MDE to customize your bands and they will be shipped to you.
I haven't had any issues booking through Expedia, and have found some good rates going through them.
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