basically in your root folder (the publish_html) you should not put any of your websites. lets say you have 2 website, web1 and web2. create a folder public_html/web1.com (the .com is just a common convention) and public_html/web2.com.
put each website files in each folder, remmeber that each website has it's own files,framework,.htaccess etc.
the routing for domain web1.com to the folder web1.com and web2.com to the folder web2.com should be in the server itself, in the vhost, NOT in the htaccess. if you are using cPanel you can just go to add domain and when you add a domain you can set the folder for the domain. so define a new domain web1.com and add it to public_html/web1.com. same for web2.com