Hosting programs

Hi all,
Firstly, I'm not sure if this is the correct forum to post this message. If not, can a mod move it to it's correct place.
What is the best way (via PHP) to achieve the following?
Scenario:
Let's assume I have developed a Help/Knowledgebase system whereby clients who purchase the software are hosted on my servers. Therefore when they create an account the program will run and function on this server.
My question is in regards to the administration side of things.
First question, what would be the best way to run such a service? If i have a bunch of clients with accounts would it be best to have the program read from one source or would it be best to create a directory for each client and hence have the program run from their (therefore each client would have their own sub domain).
Question two. If it is better to host the programs seperately how would i go about applying updates/bug fixes ect. If they are all seperate is there a quick, resourceful way of doing this in an automated kind of way...i really don't have any clear idea of what to do in this situation...i would really be interested in hearing what other folk would do in this situation.

Regards,
camcim