In the center of the KeySwapper control panel window you'll find a list of all “HotKeys”. To set a “HotKey” just double-click one of the items in the list.
On the bottom of the window, there is an On\Off switch (that will either say “ON” or “OFF”). There are also three buttons; clicking the printer icon will allow you to print a list of all the “HotKeys”, clicking the “Help” button will bring up the on-line help, clicking the “Prefs” button will allow you to set preferences for KeySwapper.