In lieu of my suggestion on reddit:
"Sewer systems would work similar to the current subway systems and highways. They could even be placed under highways/roads/sidewalks so functional manholes could be added.

Here are some concept images if you're interested:
http://i.dailymail.co.uk/i/pix/2012/07/24/article-2178141-1431C7E8000005DC-67_1024x615_large.jpg
https://vignette.wikia.nocookie.net/fallout/images/f/fc/County_sewer_mainline.jpg/revision/latest/scale-to-width-down/640?cb=20110619205956
https://rachelsigner.files.wordpress.com/2011/09/photo-by-steve-duncan.jpg?w=600&h=400
https://static.planetminecraft.com/files/resource_media/screenshot/1234/2012-08-20_164817_3324564.jpg
http://www.img5.9minecraft.net/img/sewer-boat-race-minigame-map-for-mcpe-2.jpg
http://www.img5.9minecraft.net/img/sewer-boat-race-minigame-map-for-mcpe-2.jpg
https://static.planetminecraft.com/files/resource_media/screenshot/1234/2012-08-20_164831_3324566.jpg
http://i.imgur.com/cdSsbhj.jpg
https://i.imgur.com/hW9bQUs.jpg
Thank you for your time and possible consideration :)"