The process of Search Engine Optimization (SEO) has changed greatly over the years, but SEO considerations still remain a critical part of site design. Search engines use crawlers or bots to follow links around the web and build large catalogs of webpages. Typically, you only have to submit your homepage and the bot will find the interior webpages. A directory, by contrast, is a hierarchical collection of links primarily to websites instead of individual web pages.
The structure and format of your webpages influences how high you appear on the SERP's (search engine result pages). You can use various tools to improve the structure of your pages, which may improve your ranking. The primary driver of placement, however, remains inbound links to your site and the (subjective) editorial judgments of the search engine editors.
The future of SEO remains in flux as the main search engines have worked to transform themselves into what would better described as "answer engines," leaving a reduced amount of traffic available to actual websites.