If you click 'match' to the transaction in the banking section then this will record the payment against the invoice/bill and you will not need to record this manually through 'Invoices'.
Adding the deposit to your Sales of Product Income will give you two incomes in total since you cannot apply this transaction to any open invoice.
If you need to apply the deposit to an invoice, you need to add the transaction to the Accounts Receivable.
To know more about the process of linking a deposit to an open invoice, check out this article: How to link a deposit to an invoice.
If there's anything else I can help you with, please let me know. I'll zip right back to help you out.