Ideally you should think about the structure of your website before you start coding your web pages, as once you’ve implemented one method it is tricky to change things around at a later date.
I recommend that when you design your structure you try to keep the structure as flat as possible. This does not mean that you should put everything in your root directory for best results, but just make sure the structure goes no deeper than two or three levels deep. Below is an example of a flat directory structure with two levels: -

This would mean the URL for page three on theme three would be:
http://www.mydomain.com/theme3/page3.html
You should not however design your structure like this: -

The URL to get to theme 3, page 3 will now look like this: -
http://www.mydomain.com/Theme1/Theme2/Theme3/page3.html
When you organise your structure you should try to maintain similarly themed pages in the same directory.
The main reasons for keeping a flat directory structure is because search engines might not deep-crawl your site. That is, when a search engine visits your website it might be set to crawl only to a certain depth of your website. So say for example you have a new website, the search engine might only crawl to a depth of 2, so in the case of the vertical page structure above only Page1, Page2, and Page3 of Theme 1 will be indexed by the search engine. The other pages might as well not exist! Whereas if you’d have the flat directory structure then all of the pages on your site would have been crawled.
When you’ve finished your website, it is a very good idea to create a sitemap. A sitemap provides a link to all of the different pages on your website from one single page. This means that the search engine (or a person) can jump to any other page on your website from this one single page.
If you link to the sitemap from every page on your website then it has the effect of interlinking all of your pages with each other. This means that the search engine will attempt to crawl every page on your website.
So now you’re thinking, ‘well if I make a sitemap then I don’t need to be concerned about my page structure’ Wrong! If you remember, search engines often only crawl to a certain depth, so when it finds a link on your sitemap to
http://www.mydomain.com/Theme1/Theme2/Theme3/page3.html
it will disregard it as the depth of the web page is greater than its maximum crawl depth.
I hope this guide has helped you understand how important creating a good page structure is, not only for easy navigation for people browsing your site, but also from a search engines perspective. In this next guide I will go into a bit more depth on the subject of Google PageRank - one of the most overrated factors in SEO.