The GUI seems to offer only "Process Queue" and "Pause Queue" Pause queue stops all activity immediately. I'd like to suggest there be a "Pause After" type option to finish transferring the file(s) in progress, but to not start any new files.
I'd also be wonderful, but I'm not sure FTP in general allows it, if when the queue is paused mid file, that subsequent hitting the "Process Queue" would complete transferring the file from where it had be paused.
Todd