How to start from Scratch ?

[eluser]PhilTem[/eluser]
Did you really read the user's guide? These questions should actually be answered within the first view chapters.

But anyways, if you want to create different/multiple projects, you just use the files and folders in the codeigniter download-file and put them into each project's folder. From there you will create every necessary controller, model, library, helper, view, ... to serve the content of your app

Seriously, read the user's guide. It should give you a hint of what CI is designed to be used for and what you need to do in order to achieve certain tasks.