The short answer is no, your sewer/wastewater meter is not measuring any water consumption, and therefore it should not be included in your water metrics.
However, you may still want to track your sewer meter, especially if you are metered and charged separately for sewer/wastewater. If you decide to track your sewer/wastewater meter, make sure that you do not include this meter in your metrics (the "Change Meter Selections" button on the Water tab allows you to tell Portfolio Manager which meters we should include in your metrics). For example, you may have some sub-meters that you want to track, but they are duplicated in other meters, so you don't want to them count towards metrics.
If you are metered and charged separately for sewer or wastewater, it is most likely to deduct the water that you use on site which doesn’t enter the sewer system (such as water used for irrigation or evaporated in a cooling tower).