I just filed an amended return and now it is saying I owe $1000. I don't understand how and did I do something wrong?

What is the reason you are amending?

Is that the tax due on the actually 1040X line 20?  Ignore any 1040V vouchers.  That is for the original return or what the original return would have been if it didn’t need correcting.  Don’t pay the amount on the 1040V.  Pay the amount on the actual 1040X.

Did you get the refund from the original return or pay the first tax due?  Be sure those show up on the amended return.  You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 22 should be your additional refund.  If you paid on your original return it will be on line 16.  If there is an amount owed with the amendment, it will be on line 20.

What you MAY have done wrong is to file an amended return TOO SOON.  You should not file an amended return until AFTER the IRS has completed processing your original tax return (then it is --best to WAIT until your refund is received, or your payment of tax due debited from you account).  

What you need to do now is WAIT until your ORIGINAL tax return is processed.  An amended return takes 6-8 weeks to be processed.

Also, an amended return MUST be PRINTED and MAILED to the IRS.

When mailing a printed return it is always a good idea to go to the Post Office and mail it 'Certified' with 'Return Receipt'.  That way you will have proof that they received it and when it was received.