Recieving Invoice Payments

Recieving Invoice Payments

Say I invoice customer X $1000.00. I recieve a cheque for them and therefore have a bank deposit for $1000.00. If I tell Zoho Books this deposit was from Customer X it doesn't apply that to their account.
When I then apply a payment to the applicable invoices, my sales are posted twice.
How do I apply a bank deposit directly to a customers invoice or account credits?

Thanks.