I'm happy to see you're being proactive in ensuring your accounts receivables are tracked correctly! It's a stellar habit that allows you to access clear insights into how your customers pay you through powerful aging reporting. QuickBooks Online is designed to make this a simple and pleasant experience, so over-payments are automatically tracked as credits. Simply click + New and select Receive payment to record the payment from your customer, applying it to their A/R account for future use.
Hope this helps!