You need to have them setup with the original e-file.  You have to use the IRS Direct pay system to pay them after the return has been e-filed.

IRS DirectPay will let you go in and schedule ES payments for a client.   The only catch is, they only let you schedule 2 payments in a 24 hour period, so if you want to schedule 3 or 4 ES payments you have to do it over 2 days.

"entered the estimated tax information and checked the installment boxes. I saved the file and went to File Electronically and federal estimated tax does not appear"

But before you do that, what do you mean they do not appear?   

Does it show in the Client letter that they're scheduled?  You wont see them in the EFCenter anywhere, that info just gets transmitted to IRS.

You may want to call the phone number on the 8879 and call to see IF they are scheduled or not, before trying to schedule them again.

@IRonMaN  The new higher standard deduction for seniors means a lot of couples will owe $2,600 less than they estimated in April, so the September and January payments should be reduced by $1,300 each.  Just one of the hazards of setting up all four quarterly payments so early in the year.  There has probably been a post on how to make the changes, I just don't follow that issue.