Thanks for coming back, @hilltop_account.

I can share a way to track the orders and support the prepayment invoice.

You can set a current liability account and create upfront deposits or retainers. Once done, you can record upfront deposits or retainers you receive, then create an invoice.

You can apply the upfront deposit or retainer as payment on the invoice. This moves the deposit from the liability account to your income account.

You can select any of the following methods that work best for your business.

To enter an upfront deposit or retainer as a line item on an invoice:

1.    Open the customer invoice.
2.    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.    Hit Save and Close.

To apply an upfront deposit or retainer to an invoice as a credit:

1.     From the Customers menu, select Create Credit Memos/Refunds.
2.     Select the customer or job.
3.     Click the Upfront Deposit item you created.
4.     In the Amount field, enter the amount of the deposit or retainer.
5.     Select Save and Close.
6.     In the Available Credit pop-up, select Apply to an invoice and select OK.
7.     In the Apply Credit to Invoice dialog, click the invoice to which to apply the upfront deposit or retainer and select Done.

 Please visit this article for further details of the steps: Manage upfront deposits or retainers.

If you need some information about managing your desktop account, you can visit this article for your future reference:Help articles. You can click each to view them.

I hope this helps.