" just as normal php.ini file. That would be your template of php settings for CGI/FastCGI mode
2) when new webspace/subscription is created in Plesk, it will take /var/www/vhosts/.skel/0/conf/php.ini and put it into .../domain.tld/conf/php.ini. In this file you can safely tune settings of the specific vhost - Plesk won't overwrite them
3) the instructions you put in .../domain.tld/conf/php.ini will be included in .../domain.tld/etc/php.ini file (which also includes open_basedir and safe_mode settings from the panel settings).
So now you have desired content in .../domain.tld/etc/php.ini which is applied to your vhost if run in CGI/FastCGI mode.
Let me summarize:
1) in .skel you have conf/php.ini which is a template for all your sites. If you put etc/php.ini in .skel - it won't wor, Plesk will overwrite the file.
2) in domain.tld you have conf/php.ini which is your settings for the current vhost. Settings from this file are included into etc/php.ini and merged with other Plesk settings.
Would it help you?
NOTE: This php.ini is only for CGI/FastCGI. Another file and another customization approach is required for mod_php, details can be obtained from "Advanced Administration Guide"