The best way to install APC on cpanel server is from source because the pecl installation many times fails with compilation errors ..
What is PECL?

PECL is a repository for PHP Extensions, providing a directory of all known extensions and hosting facilities for downloading and development of PHP extensions.
Official website : http://pecl.php.net/
Download page : http://pecl.php.net/package/APC
1 ) SSH your server as root
cd /usr/src/
wget http://pecl.php.net/get/APC-3.1.3.tgz
tar zxvf APC-3.1.3.tgz
cd APC-3.1.3
locate php-config
It use to be in /usr/bin/php-config
php-config file is to add the existing php configuration with apc.
phpize
Next step is to compile APC with the following modules enabled
./configure –enable-apc –enable-apc-mmap –with-apxs –with-php-config=/usr/bin/php-config
make
make test
make install
Locate the php.ini file by
php -i | grep php.ini
Output :
Configuration File (php.ini) Path => /usr/local/lib
Loaded Configuration File => /usr/local/lib/php.ini
vi /usr/local/lib/php.ini
and add this
extension=” apc.so”
Restart apache :
service httpd restart
Create an info.php page in any of your domain and make sure that you are able to see the apc module listing.