The method to save an electronic check to a customer's account for future purchases is the same process that's done when saving a credit card. The first thing you need to do is to make sure you have saved payments turned on in your system. To set this configuration, just go to the left nav panel under Configure > Preferences. From there, just scroll to the "Payment And Transaction Configuration" section and ensure you have "Use Saved Credit Cards" turned on:
Once done, all you'll need to do is just go to the customer's account page to add this information in at the bottom: