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The reason that you want to make sure that you structure and organize your site in the proper way is that it will make it much easier for people to find the information that they are looking for. People are not going to search your site to find something, if it is not obvious how to find it they will just move on to another site. The key thing here is to make sure that your site is laid out in an obvious way and that there are lots of links that will take people to where they need to go.
The challenge that you are going to face when you are trying to structure your website is that your visitors are not your only concern. In order to get visitors to your site you are going to want to rank well in the search engines. This means that you are going to have to have a site that is structured in the way that the search engines want to sites to be structured. This is a structure that is easy for their robots to follow. Unfortunately in some cases this will not the same structure that you would use for human visitors.
In general the most important thing when you are structuring your site is to keep the content on each page tightly focused. Each page should be about a specific topic, information on other topics should be on other pages. The more tightly you can focus the content the better it will be. This will make it easy for your visitors to find the information that they are looking for and at the same time make it easy for the search engines to figure out what that page is about.
Once you have your pages laid out with tightly focused content you are going to want to put them into categories and sub categories. These will then be linked together so that content that is related can be easily reached from where the visitor is. You will also want to make sure that there is an easy way to navigate between categories for the visitors who are interested in content that is unrelated. It is also important to not have too many sub categories. At most people should only have to click on three links to find what they are looking for. It is better to add more categories and fewer sub categories.
A well structured websites is not going to just happen while you are building the site you have to take the time to plan it out in advance. This should be done before you even start designing the site, get everything organized into categories. The time that you spend planning your site will save you all kinds of time once you start building it.