To check in the Desktop program 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.
When you log into your account you should also see the status and if it was Accepted or Rejected, Started, Printed, Ready to Mail, etc. What does it say?