A customer pays a 48.50 bill with a 100 note. What does the cashier do on the POS?

Type 100 against Cash on the Charge screen and the POS works out the change. Cash is the one way of paying that may be over the total, because the change is real money leaving the drawer. The drawer opens with the sale, because Cash is marked as opening it. The sale is recorded as 48.50, not 100, so the Z report and Reports → Shifts and the POS show what the sale took, not the note handed over. A cash drawer POS system that recorded the note would never balance at closing. The POS and the counter tab in the docs explains the Charge screen.