If you're an admin, you can process an electronic check payment by going directly to the invoice and selecting the "Accept Payment" button on the right. From there, you'll need to select "Credit Card" to be brought to the screen where you can input the electronic check information:
From there, just select in the drop down the payment that you want to use. In this case, this would be the "Electronic Check" payment.
Here's a short video of what this looks like: