Although it's an older question, I might chime in here since I run into this once a couple of times a year. 

1. Open a payment window under the customer 

2. Click 'Apply Credits'

3. Make sure 'Process payment' is unchecked to the right of the top icons or else you won't be able to save it. Or just click cash or check so Intuit doesn't think it needs to process a card. 

- The two opposing Journal entries should now show '0' for an open balance. 

I hope that helps.