The best way I know to do this is to create a queue file(the site from your site manager will be saved in there and it will be able to connect) and then simply run it with(I don't think the local path is necessary, it's very likely saved in the queue, but I can't say for sure):
Code:
flashfxp.exe -c2 -get "e:\queue.fqf" -localpath="e:\webbackup"
If you add or remove files on the server, it may be problematic though. I'm not sure if it has to specify every files of if it can just grab folders.
I only use it to upload stuff, not backup them so maybe someone has a better way to do this.
If you can grab a list of the files on the server, you can always create the queue file manually(that's what I do).