I really don't think there is a "best" way. There are many though. Use a templating library or roll your own method. this thread [webmasterworld.com] touches on some of them, though it's not specifically about templates. It's been discussed a lot here.
Ok sure, so what is the best way to set up a framework/template? I am currently just using include files, which makes things easy to edit the site throughout, but I am very new to this, and don't know anything else.
I am currently just using include files, which makes things easy to edit the site throughout
The best part about really popular frameworks is you can find many templates available where someone else has already done a bunch of color schemes and custom buttons for that particular framework. This makes it real trivial to cut and paste your way to your first valid HTML 5 / CSS 3 site that does some really cool stuff. Took me about 2 days to hack my way through my first site that uses a fairly complex framework and after that it's much faster now that I know what and where to edit it to make it do what I want.
Basically, you upload the framework files to the server, include them in your HTML as usual, and then change the HTML to use the framework CSS classes.