I'm guessing that when you say base you mean a base axis? If so, I have done just that. I had a large rack-based shelving system, and the robot had an X and Z rail system. I set up the robot in Motosim to have an XZ base axis. It worked very well, just make sure you have accurate motor info, including rail travel lengths and gear ratios. I did have to calculate and tweak those gear ratios on the real system. I did this by making marks at known lengths on the rail, recording the distance moved according to the robot, then scaling to figure out the actual gear ratio. This may have had more to do with inaccurate data from our rail manufacturer though.
Good luck,
Scott