RankNFile - I'm not precisely following what you're asking, but I hope this will address what may be behind some of your questions.
To emphasize what lucy24 is saying... what matters in site structure is the navigation and what a page links to. It's not about the directory structure of the urls. If anything, those can get in the way.
Also, note that on site with the default home page of... http://www.example.com/
...that having a page with this url... http://www.example.com/best-toys-of-2014.html
necessarily mean that the home page is linking to the file... best-toys-of-2014.html
(I'm using the .html extension for clarity here).
I recommend that you take a look at this discussion, and pay careful attention to g1smd's suggestions, and also to deadsea's comments... How important is it to organize pages into directories? http://www.webmasterworld.com/google/4364322.htm
Yes, it is good to have a hierarchical navigation structure, but it is not always a good idea to reflect that structure into the URLs for individual content pages.
You may have to puzzle this through and read it a few times, but once you get it, I think it will be worth the effort... because I think it explains the advantage of putting files in the root. It's not about spidering. It's about avoiding url confusion when you apply different navigation paths to your pages.
Also, take a look at the Matt Cutts video... and note that injecting folders into your filepath named for keywords is not going to help anything with regard to SEO.
IMO, you should use a hierarchical structure in your navigation
... but that's got nothing to do with folders. And yes, IMO, that navigation structure does affect how pages are crawled.