Edit: FWIW yes this is PHP.
I would suggest using PHP Minify, which lets you create a single HTTP request for a group of JS or CSS files. Minify also handles GZipping, Compression, and HTTP Headers for client side caching.
Edit: Minify will also allow you to setup the request so that for different pages you can include different files. For example a core set of JS files along with custom JS code on certain pages or just the core JS files on other pages.
While in development include all the files as you normally would and then when you get closer to switching to production run minify and join all the CSS and JS files into a single HTTP request. It's really easy to setup and get working with.
Also yes, CSS files should be set in the head, and JS files served at the bottom, since JS files can write to your page and can cause massive time-out issues.
Here's how you should include your JS files:
Edit: You can also use Cuzillion to see how your page should be set up.