I cannot find what the settings are that I should use to encrypt my data for FTP transfers. I do not think driveHQ supports SFTP (Secure FTP) but I do see that it can support "FTP over SSL". What settings should I use with my FTP client (watchDirectory)? Can I use FTPS (FTP secure data) on port 990? Is it a different server setting than "ftp.DriveHQ.com"?

Yes, DriveHQ FTP supports FTP over SSL; the server name is the same:

ftp.drivehq.com

If you use DriveHQ FileManager, it also supports HTTPS and encrypted folder.

DriveHQ Encrypted Folder feature is more secure than regular HTTPS/FTP over SSL as your files remain encrypted on server. (not only during transmission)