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Here is how you pay a deposit to a supplier without having an invoice yet:

1-Enter an expense for the given supplier with the invoice number being the date you enter it. Then you enter an account that will be Prepaid Charges. You enter the amount paid and pay it the way you want.

2-Register another expense (not an article) that will be the invoice you receive then. You enter the different articles with the correct amounts and accounts, but you will ad another article that will be the Prepaid Charge in negative to take inaccount the credit portion. You will pay the balance the way you want then.