We’ve never purchased the dining plan before and I was wondering if we were to use a quick service credit at a counter service restaurant at our resort since we would be using our refillable mug for our beverage could we then substitute the beverage for a snack and then get a dessert as well?
Normally what you do is you can use your refillable mug and get a bottle of water, soda, milk, or some kind of drink and then get your meal and dessert. You would not be able to sub a drink as a snack!
I had never even thought to do this until our last trip when the cashier noticed we had a refillable mug and told me to go grab an extra snack.
This was at Contempo Cafe:
I ordered 3 QS meals and had 3 refillable mugs with me. The cashier told me to go grab three extra snacks (fruit bowl, chips, cupcake, etc.). Unfortunately for my waistline, I chose the cupcakes.
That’s really cool! 
I always grabbed just an extra drink so I wouldn’t have to spend the money in the parks I wonder if it just depends which hotel your at!
It may even depend upon the cashier you get at the resort. Like you, we had always stocked extra drinks…
With the changes they made official last spring/summer, you should be able to exchange your beverage entitlement for a snack or dessert item. We did this at our resort CS and even at in-park CS as my wife preferred ice water to soda/lemonade most of the time.
Absolutely makes using your CS credit at a resort a better deal, as you get the extra snack or dessert, many of which can even be saved for later.
So are you also able to get a snack in place of a dessert at CS restaurants?
I believe that is official policy, yes.