Or would dhtml be a better way to do this?
Ummm...what do you think you were describing in the first paragraph? That's 100% DHTML you are talking about there.
Anyway, I really don't think that popping up a separate input box for each check would be a very effective human interface. It would be very distracting to see a box pop up, enter an amount, and then wait for another to pop up, etc.
Oh, wait! You want the popup to show *MANY* places for many check amounts? Yes, that could work. And as for not knowing how many boxes to have: Easy. Just let the user enter an amount and then you automatically display the next box for the next amount. When the user hits just the ENTER key (no amount entered) that means "end of checks".
Will that work?