I too am curious why you think that you want to remove the Proto 3 electronics for conventional operation. Are you concerned about not having enough voltage or amperage capacity from your existing power supply?
Proto 3 is a four mode decoder for DCC, DCS, conventional AC or Conventional DC control. In addition to command control capability you will be giving up motor control in conventional mode, sound, the integration of sound and motor control functions and the LED lighting package plus more features. That is a heck of a lot to give up, especially if there isn't a technical reason that you have to.