After reading most issues and solutions here I couldn't get the informations I needed about having one drupal core for multiple sites. I was able to get the multiple site feature working completely using symlinks to redirect calls to domain.com/ to drupal/sites/domain.com/.
There is just one thing I can't figure out, all the info I found was saying to use sites/domain.com/files for file handling, which works fine until you go to the website itself, you will see links as http://domain.com/sites/domain.com/files/image.jpg which is not good looking.
I was wondering if there was any way to tell drupal to save all uploaded files to the sites/domain.com/files folder for upload, but still store file path in db as files/image.jpg.
This way, if file paths are saved as files/image.jpg in DB, I would be able with htaccess to redirect calls from this location to the right one using this script
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /sites/%{HTTP_HOST}/files/$1 [L]
If anyone could help me figure this out it would be greatly appreciated.