If you have made customizations to your PHP settings in Site Manager, you will want to utilize a local custom php.ini file in your new cPanel account. Please see the related KB article on that.
Your Site Manager PHP configuration file is located in /etc/php.ini
Make sure that the versions of PHP between Site Manager and cPanel are comparable. If you are going to be upgrading from PHP 5.2 or lower to the PHP 5.3.x on the cPanel shared servers, you will want to ensure that all your customizations are necessary and relevant in the new environment.