Codeigniter best practices with external stylesheets, scripts, includes, etc

[biletobe]

Ok so I've been studying Codeigniter and PHP for a week or so now and I'm ready to begin my first site. I'm wondering what are best practices for handling files that aren't Models, Views, or Controllers? Such as includes, stylesheets, javascript files (like my jQuery), etc...From the tutorials I read, I've developed a habit of taking my Application folder and moving it up one directory to be in the same folder as my System and User Guide (which I'll probably delete User Guide before going live of course). Now with includes (headers and footers) I've noticed some developers make a subdir in the Views folder, usually called Globals, and put them there. What about javascript and css files? Do I need to put them in subfolders of the APPPATH and make constants for their location?I'm trying to plan ahead. Thank you as always!