If a script or code you need to run requires you to change the PHP values that are set by default, this can be done on a folder y folder basis.  Instead of aving a master php.ini file, you can have a custom php.ini file in every folder.  Just place all the values you wish to change (no need to put all values in there if already set how you need them) in a file named php.ini and upload to the folder the code or program is in.  The configuration settings will override all subfolders as well.

Exampe: You are using Gallery PHP code and you need to change the "register_globals value to Off instead of on.  Gallery is installed to /gallery.

php.ini file in /gallery folder would have the following code:
register_globals off