When doing an amended return, the meter is automatically 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. So this amount is in addition to your original payment or refund shown on your originally filed tax return.
It's recommended to wait until the IRS has accepted your original return and you have received the refund before you amend the return.
Then once you are done, you will see a copy of your amended return. You will want to print two copies, one for your files and one to mail in. The refund meter shows your new refund or amount due to be mailed in.
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