I feel the same as you, I dont understand what the difference is either and the whole Epay thing through the software isnt clear at all either, so ive been making any additional payment needed through the IRS DirectPay website, because I cant tell for sure whats being sent with the superseded or amended return...I still feel like an amended return is a more clear cut approach to making a correction.

An amended return filed before the due date is processed as a superseded return anyhow, so Im not sure what the purpose of the superseded return really is....and an amended return you can track the status of both refund or balance due amended returns through the Wheres My Amended Return website.