I want to automate the creation process. My idea is:
1- the client creates an account in my site
2- I confirms this account and creates one wordpress instalation to my client.
3- The client logs into the admin area and chooses one pre-fixed theme and fills the wordpress with content.
Ok. My doubts are related with the file structure to this project.
If I have 5 clients, can I use 5 different sql tables connected to just one wordpress archives directory?
See that would be 5 different sites with different themes and different databases using the same files.
You should also check out wordpress multisite. You may find that the functionality is already there, and all you have to do is unlock it.
A multisite build will allow each user to have a completely custom site, and if you want, you can theme all of the sites under the same theme.
http://codex.wordpress.org/Create_A_Network