Are you using MotoSim EG-VRC or MotoSim EG?
If EG-VRC did you initalize the controller for a base or bring in a cmos? If so then you can jog the base like a real base and it will be included in the robot job. Program just like the real controller.
If EG did you bring in an all.prm? In the *.cel you use the LINER32.dll and write the robot, link, gear ratio, model to move, and axis number. Then write a robot job to move the robot and base.