Teaman,
I don't know about your drive, but "most" drives, it is one or the other for control, usually Modbus OR Di/Do, with the exception of the Stop button on the drive panel that will usually work no matter how your configured. On some drives you can set the speed reference independently of the control source selection, see your drives docs.
If you want to have the best of both worlds, i.e. use the external Di/Do and speed control externally and have it also controlled by M3,
then: It would be best for you to get an external Modbus device like Peters ModIO(it does 485), and interface your external buttons/and analog controls to it, then interface it through modbus to to Mach3, note, you will need to write some code that will take into account to be able to enable or disable the external Analog pot, verses, machs SSOVR slider, etc. You would need to do that code in the Macropump or a plugin, it could be done through Brains but, would probably be only used here to bring in/out the data to the modbus.
I would HIGHLY recommend you use the Serial Plugin modbus since you can independently address different ranges of addresses/function groups.
Scott