Do I need to make sure my files are not buried deeply in multiple directories on my server?

I read an article from 1997 that said all my files should be in the "root" directory on my server so that they are not buried deep within the site. Is this still true?

It actually was never true, although I may have been one of those spreading that myth back then! This is one of those things that many people confuse because it's sort of half true.

It doesn't actually matter where a page physically resides on your server, but it does matter how difficult it is for a search engine to find it. So when we talk about not "burying" pages on your site, we don't mean that you shouldn't have it 10 directories/folders deep on the server; we simply mean that it shouldn't be 10 clicks away from the home page. The fewer clicks it takes to get to any given page, the more important a search engine (and your user) will deem it to be. And of course, the more important they deem it to be, the more apt they are to find and index it.

Beyond just having a link to it from the home page, pages that are in the main navigation will be naturally given more weight by the engines, as you are essentially telling them that those pages are the most important in the site.