how to install second website on subfolder

Dear All, 

i hope i can get a help from you, i am new to codeigniter, i have install main website on root, and i have another website which isntall in subfolder named "onyx".


the problem i have using routes for SEO friendly, and when i install the seond website on the subfolder i won't  work. 

it shows "404 Page Not Found".

you help is highly appreciatedd

So what server softare are you using? Apache, Nginx etc
Here's examples on Apache, as it's normally what people use.

Code:

<IfModule mod_rewrite.c>
   RewriteEngine on
   RewriteBase /onyx/
   RewriteCond %{REQUEST_FILENAME} !-f
   RewriteCond %{REQUEST_FILENAME} !-d
   RewriteRule ^(.*)$ /onyx/index.php/$1 [L,QSA]
</IfModule>

Code:

<IfModule mod_rewrite.c>
   RewriteEngine on
   RewriteBase /onyx/
   RewriteCond %{REQUEST_FILENAME} !-f
   RewriteCond %{REQUEST_FILENAME} !-d
   RewriteRule ^(.*)$ index.php/$1 [L,QSA]
</IfModule>