The "Substructure Location, Elevation (Global Z)" refers to the elevation of the top of the bent cap or abutment cap (this elevation is essentially the bearing seat elevation). "Bearing Assignment, Elevation at Layout Line (Global Z)" refers to the Z elevation of the action point of the bearing. Both of these parameters are graphically shown in the "Bridge Seismic Design" manual on pages 1-13 and 1-15. The relevant figures from the manual are reproduced below, for abutment and bent:
Abutment (bearing action point at elevation -49ft, seat at elevation -51ft):
Bent (bearing action point at elevation -49ft, seat at elevation -51ft):
