For each site, you have to create a new nginx/apache config to recognize that the site exists. You must also use subdomains for each of those other sites, as pufferpanel does not permit sub folder installation nor will recognize if you add new folders to it.
@wafflesofnerds If you're using the default configuration, check /var/lib/servers and look for the JSON for your server. You'll be able to add start-up arguments there. After making the changes, restart pufferd to have those changes take effect.