Setup an ftpd that supports fxp (most default ftp setups disable this, you will need to read man pages for chosen ftp daemon for enabling it) on both servers and use FXP to transfer files from one server to the other using an ftp client that support fxp (FlashFXP for windows, probably many others). It will allow you to queue files on one server and transfer directly to the other using a GUI client on your desktop.
There may be other options, but this is the first that comes to mind with your requirements.
Tons of rsync tutorials out there. Probably are dozens of rsync GUIs to wrap it up and make it easier. Good for experimenting with at first.
Get very familiar with rsync and scp and life will be greater. Authors of both packages deserve a massive thank you. Both are used all over the place in all sorts of gadgets, appliances, geek toolkits, etc.
Nothing wrong with rsync.. does it's job perfectly. Some people report data corruption or missing files but I've never actually had such an experience.
Also, look into BTSync - It's based on the BitTorrent protocol and although it may confuse you reading through docs in the end it's a prettier version of RSync with cross compatibility for Windows/Mac/Linux and some other goodies.
Couple commands I use to duplicate minecraft servers between eachother, works for making backups too, just compress the file at the end. I should probably learn how to write scripts and incorporate this to do it for me. What this does is connect to the ftp server and downloads 20 concurrently files at the same time to make transfers faster than 1 at a time.