How to pay a supplier a deposit without an invoice?

Hello and welcome to the Community, downscars-hotmai

To record a payment on account, simply create an expense with the Category (on the Category details line) set to Creditors/Accounts Payable, with the supplier selected in the Payee field. 

This will post the payment as a credit on the suppliers account and can later be applied as payment on the invoice. 

When you have entered the invoice in QuickBooks, select Make payment and the expense will appear under Credits where you can tick to apply. 

I'm just a post away if you have further questions or require additional assistance.