You can apply amounts from On-Account to invoices 2 different ways.

1.)    You can apply thru Payment Application:  Select an invoice that you want to apply money from On-Account to by right clicking on the invoice and selecting On-Account from the drop down.  You enter the amount you want to apply to the Invoice.

2.)    You can apply thru Key Off:  Start a new Key Off and enter the customer name and the transaction date.  All open invoices will be displayed on the left side of the screen.  Select and invoice and drag it to the right.  Then click the On-Account tab and you will see the On-Account amounts sitting out there for this customer.  Click on the one you want to apply to this invoice by dragging it to the right.  You can change the dollar amount to something less the amount shown.  I have displayed what this looks like for you:

Receivables > Customer Key Offs

Click New

Open

Set Filter requirements

Open

Invoices will appear on the left.

Left Click on Invoice and Drag to the right

Click on On Account tab

Left click and Drag on account amount to the right

Save your changes.