The main location of your websites' data is defined by your VirtualHost or Server Block, depending on whether you're using Apache or NGINX. Apache uses VirtualHosts whereas NGINX uses Server Blocks.
For Apache, you'd want to look at the file(s) here:
For NGINX, you'd want to look at the file(s) here:
Find the files that are associated with your website(s) and open each file. Within each file you should see
DocumentRoot (Apache) or
root (NGINX). That's the base location of where your files should reside, so you'll want to backup those directories/files.
Additionally, if there files uploaded elsewhere, you'll want to back those up too.
Keep in mind, those doesn't backup databases, so if you need to backup MySQL databases too, you'd need to use the CLI or use phpMyAdmin to do so.