You can also manually create a queue using command line scripting if that's what you're trying to do, I create mine with a bat file by manually specifying every part of it and then load that.
You can't add files to it once you start it though(I made a feature request for
adding items to a running FlashFXP instance from the command line a while ago though).
I assume he want a command line switch to build a queue file(like specify the site, paths, file to upload and queue name and it create/append to that file the specified item) and then he can upload it by loading the queue from command line once instead of running a new instance of FlashFXP from the command line for every single file he want to upload.
Not sure about the overwrite switch though.