Black Night uses a file transfer model based on the Apple File Transfer Manager. What this means is that it's very easy to add additional file transfer protocol handlers.
In fact, if you have the Communications Toolbox installed (it's included with System Software Version 7.0.0 and onwards), its simply a matter of dropping a new file transfer tool on your system folder and selecting that tool in the "Session Settings" dialog box.
However, note that Black Night does not require the Apple File Transfer Manager, and that Black Night's built in file transfer tools will work fine without it.
File Transfer Tools are different from Terminal and Connection Tools in that you don't just pick one and save its particular configuration. All file transfer tools are always available, and the configurations for all tools get saved with your document's settings.