"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.