From what I can see there are ONLY two connection types possible. One is standard FTP and the other is Webdav. So your best option to make this connection have any encryption possibilities is to use a PuTTy tunnel and connect to the internal FTP interface from the outside. The functionality of this program is really neat for internal use, but it lacks any security for Internet use unless you use an open FTP server with passwords. Which would not be my first, second, or even third choices.
However one other choice that would work well with this type of application would be to install the "knock" package. What that does is to allow you to run the FTP server in secure mode and then from the Windows machine you run the knock client and the firewall opens the FTP ports 20 and 21 only to the IP address the correct knock sequence came from. Of course this option works well and makes the FTP server secure from anyone trying to hack passwords and such. But it lacks any encryption capabilities for the data being transferred.
If you are afraid that you might make a mistake. The chances are high that you will never learn anything.