For the search engines www.domain.com and domain.com are 2 different things. So usually, if you want to do some SEO on your website is better to choose one of those variants and redirect the other one to it using a 301 Redirect method ( to let the search engines know about this change ).
To do this you need to create a file called .htaccess, place it in the root of your server (if it does already exists don't overwrite it, just update it) and copy & paste the lines below :
a) from www.domain.com to domain.com
RewriteEngine On
RewriteCond %{HTTP_HOST} ^www.domain.com$ [NC]
RewriteRule ^(.*)$ http://domain.com/$1 [L,R=301]
b) from domain.com to www.domain.com
RewriteEngine On
RewriteCond %{HTTP_HOST} ^domain.com$ [NC]
RewriteRule ^(.*)$ http://www.domain.com/$1 [L,R=301]