Think of the dining plan as just another means of payment, like a credit card or gift card. When you go to pay for any food-related item, you can use either the plan credits or any other form of payment to pay for the food you're getting (or, in some cases, a mix of plan credits and other payments), just as you could choose cash vs. credit vs. gift card, etc.
I would always be specific with the cast member taking your order as to what you plan on using dining credits for (as opposed to cash/credit/gift card/room charge purchases) to avoid any confusion as to having the wrong type of payment applied.
Your receipt will tell you how many credits (of the type you used) remain after the purchase when any dining credits are used.