Sample .htaccess file for Joomla! installed in subfolder called joomla17

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 # Do not change this line.
RewriteEngine on

# Add the Missing "www" when the url is incomplete
RewriteCond %{HTTP_HOST} !^www\.helpdesksys\.com$ [NC]
RewriteRule ^(.*)$ http://www.helpdesksys.com/$1 [R=301,L]

# Change yourdomain.com to be your main domain.
RewriteCond %{HTTP_HOST} ^(www.)?helpdesksys.com$ [NC]

# Change 'joomla' to be the folder you will use for your main domain.
RewriteCond %{REQUEST_URI} !^/joomla17/

# Don't change these lines.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

# Change 'joomla' to be the folder you will use for your main domain.
RewriteRule ^(.*)$ /joomla17/$1 [L]

# Change yourdomain.com to be your main domain again.
# Change 'joomla' to be the folder you will use for your main domain
# followed by / then the main file for your site, index.php, index.html, etc.
RewriteCond %{HTTP_HOST} ^(www.)?helpdesksys.com$ [NC]
RewriteRule ^(/)?$ joomla17/index.php [L]

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Then, goto configuration.php and update live_site

Done