My web host has moved to php5 and during this move my site at some point was hacked, hopefully I have removed what damage was done but I wont know for a while if I have plugged all the holes I can. But since my host moved to php5 I now have to use my own php.ini file.

Which directories should I place the php.ini file into? (if I place it in my main folder it does not work its way to the subfolders) Or do I have to place it in all my folders?