Pick your first restaurant choice and go to "make a reservation". There will be a few paragraphs at the top of the booking window, and one of those allows you to link your reservation. You won't have to re-link once you've done that.
As fla4fun said, there's a paragraph on the "make a reservation" page, just above where you enter your desired date and time, that reads:
Update Your Profile
Are you an Annual Passholder and/or Florida Resident? If so, please update your profile so we can tailor your dining search.
.Resort Guests & Dining Plan
If you have a Resort reservation or would like to associate your Disney Dining Plan to your dining reservations, please retrieve your resort reservation. (Please be advised that not all restaurants participate in the Disney Dining Plan. Please check your Dining Plan information for participating restaurants.) Retrieve your reservation.
The "retrieve your reservation" is in blue and you can click on it to enter your reservation number and other info required to link this to your resort reservation.
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