Gecko is not a motion controller. A motion controller drives the gecko. Usually the PC's parallel port or some motion controller like the ESS or a PoKeys.
If the two motors are mapped to one axis (a gantry type setup), then the homing SHOULD work as I described above. So I would talk to your motion controller provider and get them to fix that.
Failing that, you could use the LUA script API to "unmap" one of the motors from the axis in question and "map" that motor to an OOB axis. Then you can home the original axis (that now only has one motor) and then home the OOB axis (that now has a motor mapped to it). Then, once all of the homing is done, unmap the motor from the OOB and map if back to the original axis.
You will probably want to read the API manual to see what functions are available. In the Axis category.
Again, the default homing action SHOULD be sufficient for you. And if it worked, no scripting would be required. That is why I suggest asking the motion controller provider to clear this up.
Steve