you need upgrade flashfxp to 4.0+
make sure connection type is sftp over ssh
in connection -> key manager -> import certificate
choose RSA/DSA key for SFTP
give a name of the certificate, can be anything
choose your private key file
enter your password if there's one
then save it
not finished yet!!!
after you save the certificate, make sure you selected it in your key manager, then you will be able to connect to your site via ssh