By default, you are provided with a SilkStart sub-domain. This usually takes the form of mydomain.silkstart.com. Often, if a customer chooses to use a custom domain (something like mydomain.com), they will ask if this will adversely effect their SEO rankings or if Google will index all of these URLs.
Search engines will penalize your site's ranking when your content is duplicated on the web. Not to worry - SilkStart sets up your custom domain as the 'canonical' URL, which means that it is essentially the preferred URL even though both URLs access the same content.
In other words, Google is not indexing nor tracking the SilkStart URL of your site, just the one that we have set as the preferred link.
For more information on canonical URLs: https://support.google.com/