Make one of your building blocks a configuration file: config.php in which you define the locations of major scripts/directories. This way, you can be consistent throughout the whole site and simply refer to the constant or config[value] the user set earlier. This is very common practice and will also ensure consistency, cohesiveness while still let you loosen the coupling.
Plus, when you document your program, it will be easy for the user to understand how to setup your file.
Later, if you want to get really fancy, you could even have an installation script that is interactive with the user and sets the variables as per the user's request.
Alternately, you could create some kind of rc file like your own .ini file. There is a project on www.phpclasses.org that takes care of reading .ini files for you. Again, you benefit from centralized configuration settings without hard coding it into obscure spots.
