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On the Device Template, add the command group 'Internal Ruby Commands'. Choose 'Advanced, Devices' from the menu, and select the PC on which you want to run your device--whatever PC the external hardware is connected to. Choose 'Create child device', and add an instanceof your new device template. Choose 'Wizard, Devices, Generic Serial Device' from the menu, select your device, and choose 'Edit Ruby Code'. Fill in the blanks for implementing each command, and also for how to handle incoming data, process idle messages and so on.
The documentation for how to do this with GSD is here (todo)