There's no interaction between the ATC taxi instructions and the Follow me car, sometimes they'll use the same route (provided of course you selected the same parking in GSX as the ATC) sometimes they will not, but it can't be changed.
If, but ATC, you mean "human ATC", this would be even more complex because, the FSX ATC doesn't really have any notion of which taxiways to use depending on which runways are in use for departure or takoff, and I don't see how could be possible for a living ATC controller to interact with the GSX Follow me car on a remote user system, without a very complex client-server interaction, which would be ideally able to handle diversions due to changing conditions, conflicts with other airplanes, etc.