Use absolute paths in your HTML/CSS, e.g.
<link rel="stylesheet" href="/css/styles.css" />
^--- start at top of site document root
<img src="/images/kittens.jpg" />
^--- start at top of site document root
Then it won't matte WHERE you put your scripts, the hrefs/src's will always start at the TOP of your site's URL-space and work their way down.
What you lose from this is the ability to host this particular site in a subdirectory, e.g. if you decide to move it to
http://example.com/oldsite/index.php
all of your paths would in the href/src would have to re-written to say /oldsite/images/kittens.jpg
or /oldsite/css/styles.css
.