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Web Hosting and Cloud Computing Control Panels
One thing you may want to do is go to Limits and Validation -> FTP Directory Restrictions and restrict users to their home directories for all virtual servers.
As for FTP software to use: whatever they are comfortable with. They just need their username, password and domain name to configure their software. I usually use Filezilla myself.
They will want to put all of their web accessible files in the public_html directory.