How can record a single payment from a customer that pays an invoice & also credits an overpayment without messing up my bank rec & showing as 2 separate payments.

Hello, jonathaneshaw. 

I hope you're doing well. I'm here to help you record the customer payment. 

It looks like the whole exchange would lead us to create multiple transactions. It isn't entirely a single payment. For the two payments showing up in your bank feeds, are those the customer's overpayment and the refund? I'd appreciate any clarifications with this. 

For a brief overview on how to do this, we can create an overpayment for the invoice (assuming you already made an invoice). An unapplied payment (a negative balance) will appear in the customer's profile. Here's a step by step process: 

1. Go to the + New button, then choose Receive payment. 
2. Select the customer's name under the Customer drop-down menu. 
3. Add the payment method, then choose a bank where you want to deposit the payment to. 
4. In the Amount received box, enter the exact amount that the customer paid. 
5. Check the invoice under Outstanding Transactions. 
6. Add a memo or reference numbers if needed.
7. Once done, click Save and close. 

I take it that this has been refunded back to the customer (hence the two separate payments that appear in your bank). In this case, we can create a cheque, then link it with the unapplied payment. Here's how: 

1. Go to the + New button again, then choose Cheque. 
2. Select the customer's name under the Payee drop-down menu.
3. Choose the bank account where the refund was taken from. 
4. Choose Debtor as the account under Category.
5. Enter the refund amount.
6. Add memo and other important details.
7. Once done, click Save and close. 

To link it:

1. Go to the + New icon, then choose Receive payment. 
2. Select the customer's name again. 
3. Tick the Cheque under Outstanding Transactions section.
4. Under Credits, check the Unapplied Payment transaction.
5. Once done, click Save and close. 

I also take it that you still haven't reconciled your bank. In this case, we can match the overpayment and the refund with the transactions we created in QuickBooks. 

After this process, you can start reconciling your bank. 

If you have questions about processing customer payments in QuickBooks, please let me know. Though, I'd be more than happy to listen if you have other concerns. 

Thanks very much for taking the time to help.   To answer your question. Customer pays me £120. £100 pays an invoice. £20 is recorded as a credit in the customer's accounts receivable account.  My bank  rec shows 2 separate entries of £100 and £20.  I would like the bank account to show one item - a payment of £120 - which is what actually happened. Can you suggest a way of recording the transaction so the bank rec shows a single payment of £120?  Thanks.