I called the IRS yesterday and was told that to fix the mistake I just need to do my regular 1040 form and write 'Amended EIP Return' on top, however, back in April, before I stupidly use the nonfilers tool, I had already mailed in my paper return, which has yet been processed by them and I am not sure if it was received or not. Can't track the status of my return from the IRS website either, it says cannot provide any information...Can I mail another return with 'Amended EIP Return' on top with USPS priority mail, so I can track the arrival of my returns, will that cause any problem for mailing it twice?
There is no need to mail another return with those words on it. The IRS will figure out that the return you already mailed is your "real return".
You can't track a mailed return until the IRS starts processing. They haven't processed mailed returns for many weeks. Yours is likely sitting unopened along with the millions of other mailed returns that haven't been opened. The IRS has promised to get to them in the order they were received.
See this info about the current status of IRS operations:
https://www.irs.gov/newsroom/irs-operations-during-covid-19-mission-critical-functions-continue