How to Do A Simple Refund on a Client Over-payment

In this case, the client has made a payment in excess of the amount charged resulting in an unallocated amount.

You have entered a client with a standard charge of, say $120. The client does not have insurance and is responsible for the full amount.
You create a charge and then enter the payment. The client has brought a check for $150.
Enter the payment amount of $150 and then the amount paid toward the encounter.

After clicking OK, you will be prompted to create a credit or change what you have entered.

Click Yes to create a $30 credit. The client balance will now show a $30 credit balance.

You can use this credit or amount in escrow toward the next visit (say, if the client comes in for a second visit and pays $90, you can use the $30 credit to complete the payment in full.
In this case, however, we will refund the amount in escrow since no further visits are needed.

To do a refund, open the ledger and select Refund. 
Enter the refund amount of $30, the type - Refund, and be sure to enter a note explaining that the refund was due to an over-payment. Providing details in the memo will help you later to see what charge and payment the refund was associated.

This demonstrates a simple refund. 

See other articles for refund procedures for more complicates use cases.