Hi cbryant,
Your seed word, which is your main keyword phrase that your site will be centered around will undoubtedly be used throughout your site. But you will also be creating additional pages on related terms and your goal is to also rank high for those and other "long tail keywords (keywords that are less competitive). So for example, your main keyword phrase may be "low fat desserts" and that may be the main phrase you want to rank high for. But you will also be creating secondary pages on related topics where you will aim to rank high for those keywords as well.
So each time you create a new page you will consult with the brainstorming tool. Once you start getting traffic from the search engines you will find that you will be found for hundreds or even thousand different keywords that perhaps you weren't even trying to rank for.
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