Yes, fire water lines should be included in Portfolio Manager because when properly maintained and under normal operating conditions, their use is minimal. If their use is not minimal, you probably have a leak.
If you have a leak, you should count that water use in benchmarking.
However, if you have an actual fire, the water used for the fire should be estimated and subtracted from your benchmarking. Currently you can’t enter negative water bill entries, so you’ll have to subtract the estimated usage before you enter it into your water meter.