Thanks for joining the Community, drcarolynhinkle.
You can link payments with invoices by accessing their records and choosing the appropriate outstanding transaction.
Here's how:
- In your left navigation bar, go to Sales, then All Sales.
- Find and click on the payment you want to apply to an invoice.
- Under Outstanding Transactions, tick the appropriate invoice(s).
- Select Save and close.

I've also included a detailed resource about entering invoice payments which may come in handy moving forward: Record invoice payments
If there's any additional questions, I'm just a post away. Have a lovely day!