In this Google Webmaster Tools video, Matt addresses how a webmaster can make sure Google recognizes and indexes pages on a lower and deeper website level. He mentions that the question is a bit ambiguous in terms of whether the user is referring to pages that are far away from the site’s root page. In this case, a best practice is to create links directly on the root page to the deeper pages that the site author wants to promote for search engine indexing.
The video also explains that Google’s algorithms don’t distinguish different page depths in terms of their placement in site directories, at least not to a noticeable degree. What the search engine does recognize is page rank in terms of how many other websites link to the root page of a given site. If the root page contains links to the deeper pages, this will help increase the page rank of those as well. Keeping these pages only a few clicks away from the root page is a good strategy because Google will only crawl and index website subpages to a certain level before stopping.