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No, it sounds like you're on the right path.
If you have an active merchant account, you can send Online Invoices which will allow people to pay them via credit/debit card or ACH.
If YOU want to do the payment, that's another screen. If its for an invoice and you're processing a payment with their bank info, you would go to Receive Payments and select CHECK as the payment method. You should get a popup box below that asks for their bank info.