Is this a convenience store? Typically on my own dime, if I know it's self-serve, I fill up my coffee first to save time. But if you're unsure and the instructions say to order 'coffee last,' then I'd just do as you're told and tell the cashier you'd like to add coffee, then self-serve yourself after you pay.
Shopping the Greater Denver Area, Colorado Springs and in-between in Colorado. 33 year old male and willing to travel!