It depends on your university. From what I know, right now WES is accepting documents via email almost from all universities. I got same done from my university and that is the quickest way to get ECA done. Just check with your university and as long as they send your documents attached with your reference / application number it should work.
Did your University already know how to send the documents electronically, or did you provide them with an E-Mail address to send it to?