First, create a new payment method in Data / Payment Methods called ‘Account Opening Balance’ or similar.
To add a debit to a customer’s account go to Sales/Invoices/New
Call up the customer in question.
Go to the Payments tab of the invoice and choose On Account.
[You may need to create an account for the customer at this point.]
Enter amount they owe you, as below, where the customer owes $100:
Then choose the Account Opening Balance payment method to balance the invoice.
You will see similar to below on the Payments tab:
This will leave the customer owing you $100 in this example.