My account was hacked before and I was told that the hackers did it through FTP. Doteasy told me to scan my computer and clean up my files. They were very helpful with the whole process. Finally I had to reset my account and re-upload my files. They said that uploading files via the file manager tool from cPanel would be a more secure way of uploading my files to the server.
Yes, the file manager is a more secure way of uploading your files. I would also make sure to keep my computer free from any viruses and to regularly update my login password as this is the best way to secure your account.