Need help understanding how to amend an already amended return

I e-Filed my original return, which calculated that I owed around $14K.  Later that same day (ouch) I got a letter which contained info showing that my employer had already withheld/paid the taxes as part of my normal salary.  I filed an amended return showing that the IRS actually owed me $15K instead (a difference of $29K!).  Just after tax day, the IRS withdrew the $14K from my bank account as payment for the original return.  Then, just this week I received a check for the $15K amendment.  I had naively expected the overpayment of $14K would be included as well.  So, I'm still short $14K - how can I properly file another amended return - this is a weird situation.