Actually, if you have limits set up, it's "normal" practice is to reference the machine every time you start it up to "home" the machine to a known position. This way your limits are always in the same place.
With that said, some do not use limit switches at all and just "zero" the machine where they would like it to be zero'd using a reference point on the material or table for each job. This means you would not set up any limit switch settings in Mach 3 and then when "Ref all" is hit, it just zeros the position in the current location.
Dave