Whenever an internal server error occurs, the error will be added to the Error Log in cPanel. (cPanel Error Log). This will help you pin point the error. In most cases it will either be a permission error on a bad command in your .htaccess file (remember that all php values have to go to your php.ini file).
Directories that require writable permissions will no longer require 777 as permissions and suPHP will refuse to write or read on directories exposed with such permissions, make sure you chmod them to 755
Basically suPHP will refuse to serve any pages that are at security risk, for example with 777 as permissions. (will generate an Internal Server Error)
