In the first place you didn't need to amend to add the estimates. The IRS should catch that and add it in for you. Then filing a second return would reject. So maybe the state efile didn't go though the first time. Did you get Accepted emails for the first efiles federal and state? So don't do anything now. Sounds like you might be good.
Did your first federal efile get accepted? For the Desktop program you have to check the filing status inside the program. (But that hasn't been working right) Open your return and go up to menu item File > Electronic Filing > Check Electronic Filing Status
When you efile you get back 2 emails. The first email only confirms the transmission. The second email says if the IRS (or state) Accepted or Rejected your efile.
