No, at this time Portfolio Manager requires all water meter entries to be positive. However, we are looking at ways to enhance this capability in the future for negative water.
In the meantime, you can subtract the negative values from a previous entry. Please maintain a copy of the original bills so that if negative water meter entries are permitted in a future system update, you may revise the data accurately.
Water use information is NOT included in the calculation of the ENERGY STAR 1-100 score, or any of the energy metrics.