No, I didn't have to wait until the snack credits were gone before substituting. I just told the cashier that I wanted to use a qs credit for these 3 items when I got to the register. Back home today but we did substitute all over the place until the end of our trip. We even used a qs credit for 2 Plaza sundaes and a float yesterday at the MK ice cream parlor. Se went to the Intermission food court (staying at ASMU) in the evening to use up our leftover credits since we had to leave before 6am this morning and we left with 25 snack items since we had 4 snack credits and 7 qs meal credits left (family of 6 with picky eaters...)
And to reply to people wondering about double substitutions, especially at the food court with the refillable mug, yes, you can get 2 snacks with your entree instead of the drink /dessert combination. We did that a few times : meal with candy and chips, meal with cheetos and boxed cookies, meal with 2 chips, meal with 2 bottles of water for the parks later (only one bottle with breakfast though)