I\'m copying this question from over here: http://getsatisfaction.com/cyberduck/topics/can_i_use_sudo_over_sftp_with_cyberduck
I am having the same issue and finding it
I think the best solution is to use your sudo in ssh to modify permissions. You could even write a small shell script to give you access while you are working and set the permissions back when you are done.
I am actually curious if there is a better way to do this, but I am pretty sure that there is not.