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Short Answer: Using the Additional Customer Payments option under Receipt New. 
 
Explanation: Within Receipt New, enter in the Payment amount in full under the customer making the payment.
 
 
Under Additional Customer Payments, click Add Customer Payment.  Enter the customer and the amount to apply.
 
 
 
Note:   Payment amounts entered for additional customers will be posted as “on account.”
 
 
You may also move all or part of the balance to a different customer account using Add Customer Payment.