That'd be confusing, using the same terrain for different sewers. I'd personally suggest using the space to make different areas.
For actually using the same terrain 3 times... just set some sort of marker, whether it be a switch, a counter of some sort, unit commanding, or whatever, when you enter the sewers from a specific place. Then have all create enemy triggers associated with whatever marker is set, saying which "sewers" you are in.
Makes me think of Diablo II Act 2 sewers