Adding files to public_html

My goal is to change the domain name of my website so I’m cloning my site to do that. I have read instructions that say I need to put the 2 files created by your plugin into the public_html section of my host provider. Inside of my public_html, I had created a folder for my new domain. Can I put the 2 files created by your plugin into that folder? Or do those 2 files need to be put outside of any folders in the public_html? Thanks.