correct layout structure

[eluser]Uplift[/eluser]
What is the correct layout structure for views?

i can view my index.php fine, but when i go to something like index.php/blog/ or whatever then all links fail so i get no includes, css, or js.

/application/views/ (home page, etc..)
/application/view/includes/ (header, footer, sidebar, etc...)
/css/
/js/
index.php

afaik everything is relative to index.php

Would i need use full paths for linking everything? I was hoping to avoid this because at the moment i have code igniter in a temp directory before i go live i don't want to edit full site and remove it's directory prior to going live.