Yes you can, but you will either have to contact the 3rd party, or call Disney and see if they can give you the Disney reservation number. A disney reservation number starts with a "4".
I recently had a reservation I booked through Orbitz. After I waited about 24 hours, I was able to call Disney (407-939-7671) and they gave me my Disney confirmation number which I then used to link my reservation in MDE.
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