To set a vessel's transponder frequency, using the COM/NAV Receiver MFD and edit the XPDR line.
To find a vessel's transponder frequency without changing focus to it, use the Object Info window (ctrl-I).
To track a transponder, use the COM/Nav Receiver MFD to tune a nav receiver to the transponder frequency. Then use the Docking MFD (with shift-n to select which receiver is in use) or the Docking HUD (with ctrl-R to select the receiver). Note that transponders do not have infinite range.
See also: http://en.wikipedia.org/wiki/Transponder