Auto upload (ftp) video file once it's finished encoding
Maybe someone will chime in with an app suggestion that directly fulfills your need, but here's a temporary workaround - a bit convoluted, but should work.


Create two folders A and B.
Set folder A as the destination folder in the encoder.
Apply a suffix to all the output files being generated, something innocuous like ENC e.g. Clip2015-09-25-23232-ENC.mov - this step assumes that there may be other non-actionable files in the folder. Skip if not so.
Set up a batch job that runs periodically, whose first command is to rename all files with the suffix, like by adding a prefix or another suffix. And whose 2nd command is to move all files with the new prefix to folder B
While the encoder is working on a file, it has a lock on it, and so only completed files will get renamed. And only those will be moved to B.
Use any of your aforementioned FTP apps to watch folder B and transfer files.