There are a few ways of doing it:

1) a packaged addon for cpanel, plesk, etc that a user can self install and remove at a click of a button.

2) a custom script that runs with the skel. dir when an account is created and does a install based on pre-defined information.

3) custom page function that will do all install functions with form input.

The later is the method most have tried and ran into problems with scripts setting permissions, etc.

Boonex has a cpanel add on , although it see more doesnt work very well (we are modifing one of our own to solve some issues) .