If I filed a return and have received a refund but need to amend for a lower refund, do I pay with the amended return or wait for the IRS to bill the difference?

[rbfrrll]

The amended return only shows the lower refund amount but not the difference between owed between the old and new refund amounts.

[AndreaC1]

@rbfrrll it show as "Refund" or "Balance due" after you amend the return? And see my full answer below.

[AndreaC1]

When doing an amended return, the meter is reset to zero and may show odd numbers until all of your changes are entered. When you're finished with your changes, the refund meter shows any additional amount owed or refunded to you. This amount is in addition to your original payment or refund shown on your originally filed tax return. 

If you owe which should show in red/gray and say balance due; you will mail your payment that you owe along with that amended return. If you are due an additional refund, it should say refund and show in green. This link shows you how the math works when you are doing an amended return How does the refund math work on amendments?

Once you mail an amended return, it can take up to 3 weeks before it shows up in the IRS's system. So give it that amount of time before you start checking for any updates on it. After 3 weeks, you can go here Where’s My Amended Return? to check the status of it. 

Amended returns can take up to 16 weeks to be processed once they receive it. And you can find a list of frequently asked questions, about amended returns, here Form 1040X, Amended U.S. individual Income Tax Return, Frequently Asked Questions