In each ANSYS interactive simulation, a log file is created. You can edit the file for changing the parameters and save the log file as a diffent file name. It should not be same as the job file. 

Now in batch mode, you run the newly created file using command

/input, new file, log,  ...

Establish the whole model before analysis, then use element birth and death technology to kill some elements that are not included at first step. Then active the death elements to change the "Geometry" selections at next step.