Patrick, This is something I have not thought of. I have seen a relay system that allows for an either / or situation where you can keep the maunal switches for a backup system in case the magic electron box fails (could be done without relays but that would invite potential for backfeed of power thru the system if both were on at same time.
I think you are looking for the ability to control your devices with manual switches for nostalgia, but have the added benifit of automatic shut off due to low battery voltage and other programable goodnes contained withing the Switch Pro? you could simply run the outputs from the Switch Pro to each of the manual switch inputs, then configure one of the Switch Pro buttons to act as a master switch (i.e not connected to anything, just allowing for one buton press to activate the rest of the circuits to energize the outputs to your analog toggle switches. now you can program each individual output for dimming, strobe, timed power off etc and they are on all the time, with on/off control via the rocker switches. All would turn off when you take out the key, or after a set time, and would reactivate when ignition turns back on. would also allow you to use triggers inputs from high beams or other items to control your driving lights with high beams etc.
Have two of the Switch Pros and love them for the most part (the app is kind of a pain for every day use, but works ok for programming.)