There are two recommended ways to use jCore server:

1. Using for multiple websites by installing jCore server in a global place for e.g. /var/www/jcore/ with all client sites having their own home directories, for e.g. /home/client1/public_html/ and having read access to this path. This way even if an account gets compromised you won't have to be worried about the other clients nor about the jCore server as only read access is given to that directory.
    
2. Using as a standalone website by installing it separately for each client to their own home directories but this way you would have to keep all clients up to date separately so this is meant only for those who don't have multiple clients.

Both of these install methods are described more detailed in the Howto -> Install -> jCore Server section.

 jCore server also contains the Official modules already, so you don't have to download these modules separately but client sites won't see these modules automatically. This is because I don't think clients should see all the modules they don't even use so for clients to install modules you would have to or copy over the module you want to their /home/client1/public_html/lib/modules/ directory or just adding the module to their db manually. The second one is recommended even if it's a bit more complicated as that way you won't have to keep the modules updated separately also, but would use the ones from the jCore server and enabling you to easily update and/or extend your modules list. To learn more about how to install modules please see our Howto -> Install -> Modules section.