The servers use a master php.ini file for all directories without a php.ini file in it. You will have a copy of this file in your public_html directory, and you can make any changes to this file, and they will take precedence over the master file. You will need to copy this file into all subdirectories within your site which have php files that you would like to affect.
You can also use this to have a different environment for different folders. So, if you want to run two scripts which have different requirements, you can put them in two different folders and then put different php.ini files in each of those folders.
If you have any further questions about configuring the php.ini file, there extensive descriptions within the file itself, and you can also find more help at:
http://www.php.net/docs.php
NOTE* If this file is not in your public_html folder, there is a way to add a new one.
1. Login to your cPanel
2. Find the Software / Services section
3. Select the PHP Config icon
4. Look for the section that says "Install Default php.ini"
5. Select the "INSTALL PHP.INI MASTER FILE" button
6. You will now have a file inside the public_html folder named php.ini.default
7. Use the File Manager to rename that file to php.ini
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