Hi!
The best approach to dealing with includes is this:
1) define a constant in a separate include file that will be included with each page, say includer.php, and place it in every folder. The constant should point to the web root of your site from all files in current folder.
define("SITE_ROOT", "../");
As you may guess, the constant will be declared differently in different levels of directory hierarchy
2) include this file in every page
3) do includes like this:
include(SITE_ROOT."inc/classes.inc.php");
If you place any of your files in another locations, you won't need to reconfigure include paths. All you need to do is ensure whether there is includer.php in the same folder and that the path to web root is set correctly in it.
Hope that helped,
Stas