Absolute "noob" questions

[eluser]Randy Casburn[/eluser]
[quote author="callumd" date="1225535658"]Also,

I'm assuming any 'images' or 'styles' folders should be hung off the application directory, yes?[/quote]

One of many possible solutions. Note that both application and system folders are outside the webserver DOCROOT...

Code:

/stuff
/ci_system
/ci_applications
  --/app1
     ---/config
     ---/controllers
     ---/models
       etc
  --/app2
     ---/config
     ---/controllers
     ---/models
       etc
/DOCROOT
  --/app1
    index.php
    .htaccess
     ---/scripts
     ---/images
     ---/css
  --/app2
    index.php
    .htaccess
     ---/scripts
     ---/images
     ---/css