Thank you for your reply however it is too generic.
Please let me clarify a couple of points:
We use Quickbooks desktop
The payment is for an invoice
When creating/receiving a payment, should I select EFT as the payment method?
Since the payment is deposited directly into the bank account, shouldn't I select the deposit checking account instead of the "Undeposited Funds" account in the Deposit To field? In your reply it says I can do either but I'm not sure which way is the preferred or recommended way from accounting perspective