Totally know what you mean! Just almost had a server quit over it today in fact. I don't want to turn off the gratuity check boxes for the same reason: I don't want the customer having to do the math after food and drinks (not trying to belittle anyone, but there were many arithmetic errors before the boxes) .
I understand square being cautious about payments tendered, but this is a really specific situation. Like, there is only one way this comes about and that is a gift card payment that uses the whole gift card but leaves a remainder of the check. Then, the remainder is paid by credit card. That partial credit total is what the gratuity is based on, which is not right. In this scenario, the grat should be based on the previous total because the customer is just going to check the box which leaves a pretty small gratuity. They never check that the total is less then the check and leave a custom tip. So the server gets the short end of the stick on this EVERY TIME. There has to be a way to fix this.
