How do I backup encrypted files to an FTP server?

Encryption requires Compression to Zip (or equivalent) file/s. You can set Level Of Compression to zero to simply 'wrap' the files in Zip/s without re-compressing them. There are also options to not compress various file types, e.g, JPG, MP3 (see Modify profile > Expert mode > Compression > Compressed).

Compression to FTP requires one of two methods, as per

Simply include Encryption settings in whichever overall method you choose or need to follow in the article linked to above.