When creating a subfolder, on an existing site, create a .htaccess file like this to automatically map the CodeIgniter urls:
RewriteEngine on RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteRule ^(.*)$ /subfolder/index.php?/$1 [L]
Source: https://stackoverflow.com/questions/7527491/codeigniter-htaccess-subfolder-problem