When you create a path with MadCam the zero-point will always be the zero-point in Rhino. If you move the fixture in the machine or change coordinate system, it's up to you so to speak.
Sometimes I zero the machine at a given point on the mould/fixture, but most of the time I set the machine zero at the same spot (machine zero) and then have the mould/fixture set at a given position. I do the same thing if I mill multiple pieces in the same run, I know the positions of each fixture (it's very to find the postions in Rhino) and the make one long tool path including all fixtures.
If there's a place to set G54 in MadCam, it's secret to me.
Hope my answer helped you!