Yes you owe the original tax due. In fact you should not amend until the fully process the first return and you paid the first tax due.
The amended return Assumes you paid the original tax due.
Then the amended return is only for the difference you get back or owe. 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.
