What I would do is if there were '(in)convenience fees' charged; and the resident uses the electronic payment for more than a one time basis; I would offer them a monthly discount from their rent equal to the fee.
With our E-Pay system, a resident is not charged a convenience fee if they pay with their checking/routing numbers as opposed to debit/credit cards.
Regarding the idea of concessing their fee, I would hate to see a $20+ reoccuring concession each month--especially if multiple residents were paying online regularly.