There are 3 php.ini in the system(debian based):
/etc/php5/cli (for command line interface)
/etc/php5/cgi (for cgi/fcgi)
/etc/php5/apache2 (for mod_php)
I don't understand why you need to move. You must configure each php.ini properly with your needs.
For example in my server ispconfig run in mod_php and websites in fastcgi. Also don't forget that you can use custom php.ini for every website.