Thanks for the replies,
When I said software I meant the assign controls interface within DCS. Using the controls interface I can assign functions to any of the buttons on the warthog and they can be different from module to module as long as they are assigned within the module level interface. Ie: hat button could be set as trim on the f-18 and look around on the f-5.
If I used the BBI-64 would the buttons, switches and rotaries be recognized by DCS and assignable within the DCS interface so they could be assigned differently between modules?
Need to find out more about the different input protocols available. Some have stated there is a 16 device limit for windows joysticks but just scratching the suface there seems to be a newer direct input api that may not have the same limitations.