Based on my experience,  hackers will usually replace / add one or more file to your website directories. Shell commands can be used to conveniently remove all the unwanted  files from multiple directories.    

find $HOME/public_html -name hackersfile.* | xargs rm -f

Replace hackersfile.*  with the name of  files added by hacker. They will add their version of both index.php and index.html. Most Cpanel webhosting allows SSH access.

More information on Linux/Shell commands/ syntax to be used available at
http://books.secs.ac.in/ShellProgIn24h/bkindexf.htm
http://www.mediacollege.com/linux/command/