I guess that your procedure cannot be done with the ngspice embedded into Eeschema. The Eeschema/ngspice interface is too limited. The main point is that you can run only one simulation at a time. Altering something, running it in addition and watching and comparing the results is not possible.
You may create the ngspice netlist by Eeschema. If your circuit in Eeschema is ready for simulation, run the first ac simulation and create a netlist. Then do the changes (to your voltage sources ?), run again Eeschema and create a second netlist. And now you may compare what has to be changed from first to second netlist and find a way to do it automatically by adding a .control script. Depending on what you want to change, commands ‘alter’ or ‘alterparam’ may be chosen. In the script you also may do calculations using both results, or plotting. Finally you may add the script to Eeschema for running your sequence automatically by the Tools->Generate Netlist File…->Spice->Run Simulator procedure.
You may start with the KiCad\share\kicad\demos\simulation\sallen_key\sallen_key.sch example on how to run an ac simulation, and then move on. An example how to use external ngspice is given here: http://ngspice.sourceforge.net/ngspice-eeschema.html#external. And of course you may publish your intermediate results here, if there are more questions.