Google will index both the domain and the “www” subdomain. That stuff is deprecated anyway. I have no idea why people use it. I understand in publication it is useful s it denotes a website.
As for the Google Webmaster Tools, if you use them then yes you can set the www or non-www part to be indexed.
If you don’t use Google Webmaster Tools then the chances are that Google will index both sites. I don’t think it’s a huge deal, especially if they are on the same IP. If they were on different IPs or even C Class IPs then you’d have trouble.
I would add the htaccess text that was stated above (assuming you’re using apache webserver with the rewrite engine enabled).