How do I get Quickbooks to link a $500 pre-payment to an invoice that's created in the future?

When you deposit an advance payment post it to the account Accounts Receivable with the customer name. Then when you create an invoice you will be prompted that there are credits available

Thanks for providing us in-depth details about linking a $500 pre-payment to an invoice, MECH Scan Solutions.

In QuickBooks Online (QBO), we handle the customer pre-payment by recording it as a retainer or deposit. This way, invoices are paid using the money from the deposits. 

To record a retainer, let's create a liability account in QBO. This tracks the retainer amount you receive from your customers.

Here's how:

1. Click Accounting on the left side menu.
2. Choose Chart of Accounts.
3. Tick the New tab.
4. Select Other Current Liabilities in the Account Type ▼ drop-down menu. 
5. From the Detail Type drop-down menu, choose Trust Accounts - Liabilities.
6. In the Name field, enter a name for the account.
7. Tap Save and close.

Once done, proceed to step 2 until Step 6 in this article to finish the process: Record a retainer or deposit.

For Step 4. Create Sales Receipt or Invoice for deposits or retainers section, just import your invoices from Saasant into QBO. Then, follow the steps in Option 2. Invoice customers for deposits or retainers section of the article provided.

By doing so, this decreases the amount in your liability account and applies the credit to your customer's invoice. This will turn the liability into an income.

I have a link here that provides you with articles about managing your customer transactions: Sales and customers gather topics for all your company's income and customers.

That should keep you on the right track. Fille me in if you need a hand with creating recurring invoices or any QBO related. I'll be here to help.