I don't believe there is a specific feature for overpayment. but you could do the following:
1 post the payment via cash receipt journal for the customer. for example 1000 usd. You'll get a payment line on the customer ledger entry showing 1000 usd, status Open.
2 from payment journal, apply the payment to purchase invoices and post. If only 600 usd has been applied and posted to invoices, the original payment line will has 400 as remaining amount with status Open.
3 you could apply the remaining amount to future invoices for that customer
Yes, after you have applied the payment to the applicable invoices, simply adjust the Amount field on the Journal or Deposit to match the actual amount the Customer has paid. The remainder will remain Open on the Customer Ledger Entries. You can navigate to the Customer Ledger Entries and use "Home > Apply Entries" to apply the overpayment as needed.
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