What to do when a customer pays an invoice with a check?

I've got you covered, @RMyrick.

You can enter the payment for them and match it to their existing invoice in QuickBooks. Follow these easy steps to get this done right away:

1. Select the +New button and choose Receive payment or Receive invoice payment.
2. Pick the customer from the Customer drop-down.
3. From the Outstanding Transactions field, select the open invoice you want to apply the payment toward.
4. In the Payment method drop-down, choose Check as payment method.
5. Once done, hit Save and close. 

For more info about the process, see this article: Take and process payments in QuickBooks Online. 

Also, to get a list of all payments and invoices for each of your customers, you may pull up the Invoices and Received Payments Report. Then, customize it so it will only show the info you need. 

Please be sure to check back in if you have further question about this. I'm always around to help you in any way I can. Have a good one.