You cannot encrypt files while they're being transmitted with FTP alone. FTP was made for transmitting files quickly, so there are no methods to do a one-way encryption on a file that you send. Only full encryption of the FTP transfer is possible, but that would leave you with unencrypted files on the remote server.*
If you want to store encrypted files on the remote server, you should encrypt them before sending, e.g. with OpenSSL or any other encryption method like putting them in a TrueCrypt container.
* The only way to have an encrypted FTP transfer itself is to do it over SSL, which is called FTP-SSL or simply FTPS. However, in order to use it, the remote FTP server needs to support this. All major FTP clients for OS X (including Cyberduck and Transmit) support FTPS.