The structure of your site is important, because it's the roadmap Google will use when it crawls your website and ranks your pages. The structure includes how a user navigates the site, how your URLs are written, and how many clicks it takes to get to your most important content. Most site owners organize content into groups, or categories. My favorite word for this is taxonomy. My editors/writers cringe when I say taxonomy ;). How you decide to group your site will impact how it works for both users, and search engines. Less clicks = better results. The closer your content is to your homepage the better the results and the better the category it's in the better the ranking value.
Say you have a bridal website and you are selling wedding gowns. You'll want to make sure your URL is something like yourweddingday.com/wedding_gowns. The content on this page should contain information about wedding gown style, designer, detail, pricing and so forth. The link should be visible in the navigation and one click away from the group of information you are trying to deliver. Having multiple clicks to get more information on designer or pricing will not work in your favor.
SEO is tricky but if you properly plan for it you will see better organic results. If you need assistance with your current site please call me to discuss.