CI Folder Structure for applications

[eluser]Unknown[/eluser]
Hello, i'm a newbie here. I'd like some suggestion about CI folder structure for sites i'm currently develop.
Let say if I have three applications that i would like to share in one CI installation, what would the folder structure looks like?how to configure CI for these three applications? for example, i want the visitor to have three roles : guest, employee, administrator.
And how do i put external files/third party such as JQuery, CSS, Javascript, etc so it can be shared to those three applications?

Thank you for your help