Hello there, PaperPanda.

Let me share with you some information on how to handle upfront retainers in QuickBooks Online (QBO).

There are two ways to apply upfront deposits or retainers to invoices. You can either enter the upfront deposit or retainer as a line item on the invoice or apply the upfront deposit or retainer as a credit.

Here's how to enter an upfront retainer as a line item on an invoice:

1. Open the customer invoice.
2. In the Detail section, select the Upfront Deposit item you created from the Item drop-down list.
3. Enter the amount of deposit to be applied to the invoice in the Amount column.
4. Select Save and close.

Here's how to apply an upfront retainer to an invoice as a credit:

1. From the Customers menu.
2. Select Create Credit Memos/Refunds.
3. From the Customer:Job drop-down list, select the customer or job.
4. In the Amount field, enter the amount of the retainer.
5. Select Save and close.
6. In the Available Credit pop-up dialog that appears, select Apply to an invoice and select OK.
7. In the Apply Credit to Invoice dialog that appears, select the invoice to which to apply the upfront retainer and select Done.

To be more familiar with managing retainers in QuickBooks Online (QBO): How to record a retainer or deposit. 

That's it. Don't hesitate to get back to me if there's anything you need. I'm always here to help you some more.