I have two scenarios. I have ave a customer who had a $100.00 outstanding invoice. He sent me a cheque in the amount of $100.01. How do I apply the $0.01 overpayment?

Hi there, 

Welcome to the Community. QuickBooks is an easy-to-navigate program that helps you to manage your accounting with ease. I'll be glad to share more info so you're on the right track with your work. 

In order to accurately record your transactions, I highly recommend consulting an accounting specialist for expert suggestions. This ensures your books remain accurate while you continue to manage your work with peace of mind. You can also get in touch with a professional using this link here. Other accounting professionals are able to see this post in the Community and this will allow them to chime in. In the meantime, feel free to check out the following article that shows you how to: Handle a customer credit or overpayment in QuickBooks Online. 

Let me know if this info helps. Otherwise, feel free to ask questions in the comments below.

Receive the cheque amount as-is and make a note in the memo section that the invoice was overpaid/underpaid.  

If you are going to write-off the 0.01 overpayment/underpayment and then you'll want to create a credit memo or an invoice to clear the open amount on their account (to bring their account back to zero).  

If you are going to ask for your customer for the $0.01 owing (or keep the overpayment of $0.01 on their account to apply to a future invoice) then you don't need to do anything else (the overpayment/underpayment will show up on their next statement you generate through QBO).