You get the amended refund separately. It will take up to 16 weeks to process and they only mail checks for amended return refunds. Did you MAIL the amended return form 1040X? You can not efile an amended return. And they only get the first original efile.
You will still get your original refund or need to tax the first tax due. Then the amended return will only be for the difference you get back or need to pay back.
The amended return will only show the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 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. When you go through the amendment section it asks you how much you paid or got back on the original return so be sure to enter it. You might need to go back and answer that question. I think it's one of the last questions in the amended section.
How to Amend
https://ttlc.intuit.com/questions/1894381-how-to-amend-change-or-correct-a-return-you-already-filed
