Suppose you receive advance payment that cannot be characterized as trust fund.  For example,  you provided paid consultation, valued $150, but offered to give a credit of $150 against future services.  This money has actually been earned by you, hence does not belong to client trust fund.  

To account for this payment in invoice, generate the invoice.  Then click on the green dollar button (Cases -> Invoices) in the invoice list.  Record a payment of $150. 

Then click on the pdf icon in the invoice list to view the invoice.  The invoice would show total of all payments recorded against this invoice.