Hi, Sara!
Great question!
When you make Advanced Dining Reservations at a Walt Disney World restaurant, either through WDW's website or by calling Walt Disney World Dining at (407) WDW-DINE, you don't have to worry about linking those reservations to your
Disney Dining Plan.
Once you've selected your Disney Dining Plan, think of it as a bank account, in which you've deposited the total number of dining entitlements for your party. Those entitlements (Quick Service meals, Table Service meals and snacks) will remain in your account until you use them. As such, when you arrive at one of those Advanced Dining Reservations you've made online, just tell your server that you'll be using your Disney Dining Plan for this meal, and he or she will guide you through the rest of your experience.
When you've finished your meal, and it's time to pay, simply provide your server with your Key to the World Card, which will be used to remove those dining entitlements you enjoyed at that meal. The balance of entitlements will remain in your account, and that total will be printed on your receipt, too, making keeping track of what you've used and what you have remaining a very simple task.
I suggest that you log into My Disney Experience on WDW's website, too, so that you can keep track of all of your reservations in one simple place. Together with the free app, you'll be able to manage your vacation details easily, and will be able to access them remotely, too. Win-win!
Send more questions as you think of them, Sara; I'd love to help!