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Just to clarify and provide an answer a bit more accurate to your question. 1. Whichever you want indexed (the www version or the non www version) you should have 301 Redirect functionality set up pointing to the one you want from the one you don't want on a site-wide basis. 2.  In GWT, you can designate that you want them to prefer the www version or the non www version. 3.  If you don't already, be sure to have a sitemap.xml file set up on your site, and submit it through Google Webmaster Tools and Bing's Webmaster Tools. 4. Having inbound links helps for ranking however it's not required just for indexing, if you submit the sitemap.xml file.  I've had plenty of sites indexed way before any inbound links existed. 5.  With both Google and Bing's webmaster tools you can review their data to see if either find any problems in your site.