Here are few points:
* One bank account can have one more more "payment documents" underneath it.
* Payment document (not the bank account) is married to a Format.
* You also attach a Format to payment profile. Pay Run will produce an output in this format.
* Only those payment profiles are available that are married to the same format as attached to the document chosen.
* You associate invoice with a payment method.
* You also can restrict payment profile to be used with certain payment methods. Only those invoices will be picked up by the pay run that are associated with the payment method permitted under this payment profile.
* Yes you can override the invoice payment method from the payment screen when making a quick or manual payment. By default the invoice payment method will appear on the screen. You can change it if you like to pay the invoice using some other method.