Moving application folder etc. out of system folder

[eluser]headdy[/eluser]
Newbie here. I've tested a couple of frameworks for my project, and decided on CI because it's lightweight and (more importantly) has the best documentation of the ones I've tried.

But I'm missing something... I've seen a lot of talk in these forums on moving folders out of the system directory, but I haven't seen any specific instructions for doing so.
At the moment I've just moved the application folder to the root and that appears to work.

Could someone point me in the right direction?