Don't -- you're just going to complicate things. The IRS already has a backlog of over 35 million returns. Filing an amendment won't speed things up. The IRS already knows they need to adjust your returns and issue a refund, but they're behind schedule. You need to be patience or else you're just complicating the matter.
You should have paid "what you owe" when you filed your returns regardless. Otherwise, their system will continue to assess interest/penalties. It was a requirement that you're supposed to pay what you owe at tax filing. You may be able to negotiate this by calling the IRS directly. But like I said, they are currently having a huge backlog and not even resources, so I am not sure if you can even get through (many people are saying the IRS is not even answering their phones now).
I'd suggest just wait and see. Or pay your balance, make a note. And then when the IRS adjusts and refunds, call them directly to address any discrepancies. Basically, you need a human to help you.
Good luck.
