ddarienzo on "Custom Registration Page that I do not want on a menu"

Hello. I am new to WordPress but I am making some good progress. I have a blog that is for members only (For a retailer association). I created a custom registration page from scratch and installed it on the root directory. I redirect non logged in users to it and it works fine. However, in order to keep the look and feel I had to copy the css (style.css) to the root directory, link directly to the header image, recreate the header text and so on. What I would like to do is create this registration page within WP framework and be able to add the main text to it, using the WP themed header and footer. When I create a New Page in the Admin window, it automatically puts it in the main navigation menu - which, of course, one would not see until they are logged it. The page that I created and works can be seen at pafr.org. I know what I am trying to do is relatively simple but I'm just not sure how.
Thanks