An example, say I develop a site for car lots, it would let them keep track of their cars online, as well as keep up their website. I should have clarified what I meant by users, when I say users, I mean people who buy a website from me, that was confusing.
So in the database, I would store information about my clients.
ex: Joe's Used Cars, joesusedcars.com, /srv/www/vhosts/joesusedcars.com/httpdocs, updates=yes.
So, what I would do in this case is write a script that would go through this "clients" table and copy the php scripts from the base site directory to the clients site directory which is stored in the database (cp /srv/www/vhosts/basesite/httpdocs /srv/www/joesusedcars.com/httpdocs). So I have a controlled, automatic update system, whenever I run the update script.
I know that this way would be easy enough, and maybe now you understand what I mean when I say including the files for the different sites.
So, when you go to joesusedcars.com it would actually be pulling the header and footer from joesusedcars.com, but it would be including the action php scripts from the base site, using the joesusedcars.com database.
So I wouldn't even have to run the update script, because anytime I change the scripts in the base site, it would automatically change for all clients, since they are including the files from the base site.
Thanks again for the input.