It depends on where the cash has come from. I have a client who does this all the time, sometimes he withdraws the cash and other times its from petty cash. You can part pay the invoice in sage. Let say is is £500 cheque and £500 petty cash, pay £500 using the current account and the other £500 from petty cash, you have to put in the figure in a column on the right from memory can't think what it is called (the one that gets filled in if you hit the pay in full button).