I not sure auto ES payments will go with an EF amended return, I personally wouldn't trust it to happen.  

Id set them up at IRS DirectPay to be sure they actually get scheduled.   I think IRS still limits how many payments you can set up on a  daily basis, to 2.  Youd have to schedule the first 2, then log back in the next day to schedule the last 2.  DirectPay gives you a printed confirmation, much more reliable than the software.