Click into your unapplied payment.
Check your "Deposit To" dropdown box. If it says "Undeposited Funds", change it to your checking account that's connected to your QBO account.
In the "Outstanding Transactions" below, you'll see a list of invoices. Select the invoice you want to apply to the payment (you can do partial payments). Click Save.
When you go to Transactions > Banking, you should now have the option to match the payments received with the deposit made to your bank.