In your case, we are interested to measure the light that is injected from the source at the output of Input_wg in the area the is shown by green light in the figure below:
We cannot measure the entire power that passes through the monitor as there will be some reflected power from gratings if we include all the simulation time. Thus, apodization can be used to measure the results at a specific time to remove these reflected power. This is important because light is reflected at the facet of input waveguides, and authors may have reported the power results right before entering the output waveguides.
You can choose “end apodization” (as you are only interested in the input power and want to remove the reflected power) for the input waveguide and “start apodization” for the output waveguides and then normalize the results w.r.t. input power obtained from the monitor.
The link below might be also useful for you to review:
I hope this was helpful.