If your account has been compromised, you should:
1) Change your cPanel password, and the passwords of any other databases or email accounts on your account.
2) Remove the hacker's files.
3) Before you upload your files back, ensure that any CMSs/Blogs/Forums/etc are up-to-date as each update normally fixes security vulnerabilities. If any CMSs you had were not up to date, this may have been how the hacker modified your files.