Customer has paid twice. cleared balance with first payment then they paid same amount again. they want to keep it as a credit on there account against a future invoice.

Welcome to the Community space, info1992.

There's no need to create a credit since QuickBooks automatically create credit when your customer overpaid the invoice. If you want to use the credit toward an invoice in the future, here's what you'll need to do:

Apply the credit to an invoice you already created:

1. In the left menu, click the + New button.
2. Select Receive payment.
3. Choose the customer, then the credit and the invoice.
4. Select another pending invoice and enter the overpayment amount in its Payment column.
5. Select Save and new or Save and close.

Apply the credit to a new invoice:

1. In the left menu, click the + New button.
2. Select Invoice.
3. Create the invoice.
4. Select + New. 
5. Choose Receive payment.
6. Select the credit.
7. Click Save and new or Save and close.

However, if you turn on the automatically apply credits on your company settings, there's no need to apply the credit manually to an invoice. Since QuickBooks will apply it to the open invoices. 

To know more on what to do when customer overpays you, see this article: Handle a customer credit or overpayment in QuickBooks Online.

Keep me posted in the comments if you have other concerns about managing invoices and overpayment in QBO. I'm always ready to help.