Before setting up an MT3DMS model in GMS, you must first build a MODFLOW flow model and generate a solution. MODFLOW automatically generates a head and flow file (*.hff) containing information on computed heads and fluxes. This file is used as part of the input to the transport model when MT3DMS is launched.
MT3DMS uses the top and bottom grid elevation specified in the Global Options/Basic Package Dialog.
When building or interacting with an MT3DMS simulation, the corresponding MODFLOW model must always be in memory in GMS. This is due to the fact that MODFLOW and MT3DMS share many of the same data structures (layer elevation arrays, stress periods, units, etc.).
Related Links:
Building an MT3DMS Simulation
Running MT3DMS