BetterPHP

I was following your tutorial on making a register and login and I was wondering how I could implement it to my site. I'm fairly new to html/php. As of now I only have a login system working with my website.

It depends on what you mean with "implement" and what your site looks like now.
Adding it is just copy+pasting, not hard at all.

As of now I have an index where my website is set up, simple website layout in dreamweaver. Do the user and init files would go in the same directory as my index file? How does the include function work? As of now I have the files in my E driver, so would I just direct it to where the files doing ? ex: include ('E:/xampp/htdocs/php_test/init.inc.php'

Well, if you've followed the tutorial you would already have a finished working website. All you need to do is move the design from the site without the PHP code ( or move the PHP code to your HTML site, that can be a bit more complicated though ).

I believe you're over thinking this a bit. If you have a PHP page and an HTML page, there is nothing stopping you from copying code from one to the other.