You can use WebJetAdmin for most of your printers; it is a GUI-based control system.
There is a new version (10) out now, which I think is Windows only, but (because it is not Java-based) is supposed to be considerably faster than version 8 (there is no version 9).
I've no experience of either version, so I can't tell you much about it, but you should be able to use it to control the sort of properties that you can set via the printer front panel (if it has one - smaller ones don't).
Alternatively, for individual printers, most modern office/departmental network models have a built-in Embedded Web Server (EWS) - just point your browser at the printer's IP address and you'll see it - it should give you much the same as the basic WebJetamin gives you.
Bear in mind that if you are FTPing files direct to the device, the files need to be in a format that the printer understands: this usually means one of:
(a) Plain ASCII text; in this case the default Duplex setting will have an effect, as will default font settings, etc.
(b) A 'print file', already formatted (by 'printing' a document, from within an application, 'to file'), and using the target Page Description Language (PDL) of choice (PCL5, PCL6 or PostScript); these files will usually contain control sequences to set simplex/duplex, which will over-ride whatever you set as default on the printer.
(c) A PDF file: some of the more modern LJ models have a PDF interpreter built-in (but it usually only works if 128MB of memory, or more, is installed); I'm not sure if PDF has any concept of simplex/duplex, so the printer default may have an effect.