It's actually quite simple....
If you fly on QNH, like most people these days, and you are doing a non-precision approach or a Cat 1 precision approach, you set the baro minima for the approach as given by the bold print in the Jeppesen or Aerad or whoever) chart. For a non-precision approach this is a Minimum Descent Altitude and for a precision approach this is a Decision Altitude. If you have a radalt (whether part of the EFIS or a separate analogue indicator) on which you can simultaneously display a radalt minimum, then you can of course set the equivalent value from the chart (or better, something like 50 feet below for non-precision or 20 feet below for precision, to account for uneven terrain on the final approach track. Whether you do this will depend on your Company procedures.
If you are flying a radalt-based approach such as a Cat 2/3 ILS or an offshore airborne radar approach to an oil platform (though I guess you wouldn't do this in your Bus or G5), set the radalt to the Decision Height or Minimum Descent Height and ignore the baro box.