Rachel, you bring up a good point that confuses many authors. I recommend that authors create just ONE website for all of their books. The main reason is because you want to make it easy for people to find you, interact with your online community or blog, and gather their contact information. In other words, a "one-stop shop" is usually a better approach than setting up several different "stores."
Authors who create several different websites for each of their books run the risk of segmenting their audience too much. This prevents their readers from finding out about the author's other books and cross-promoting titles. Also, you will generally get a higher search engine ranking with one author website that is busy with traffic, rather than multiple author websites with smaller traffic.
Having said that, you could consider creating a specific landing page or separate parts of your author website that is dedicated to each of your books. That way, you can easily direct readers to a particular book that you want to highlight - without reducing your overall website traffic.
Keep your author website simple and easy to navigate. Getting too fancy usually frustrates the visitor and reduces your book marketing effectiveness.Thanks for the question...keep 'em coming!