Login to Admin

Go to Admin -> Customers

Bring up a Customer Account

Search for Customer

Open the account

Double Click on the customer.

Highlight the customer and click Edit.

Click on the Activity tab.

Click on the Payment button. 

Enter the amount of the payment.

If this is a check payment, mark the checkbox for Check Payment.  

Enter the check number in the supplied area. 

Select the Account to which the payment will be applied. (ex. A La Carte is the default)

Select Payment.