I am the MIS Manager for a community bank, not Commerce. What are your concerns about using electronic banking for payment vs some other means?
An electronic payment should work the same for Disney as for any other bill that you pay. Just make sure that you make the memo portion of the e-check descriptive enough, whether it is with your name, hotel, confirmation # and stay dates, or a combination of them.
Honestly, the only trouble I've ever had with my electronic bill payment was with a "Mom and Pop" optician. This was easily rectified with a phone call to the e-billing company.
If you are still concerned after you send the payment, give it a few, even 10, days and then call Disney to confirm that payment was received.
The only reason I ever write a check is for my kids' lunches at school.