In order to use a rat tunnel you must first learn Possession (Level 1), then possess a rat and have it walk through a rat tunnel. The first opportunity you get to do this is also the easiest location to do it at: the start of Mission 2: High Overseer Campbell. After you step off the boat with Samuel, walk up the stairway on the left and hug the wall. You will come to a Wall of Light and just to the left of it will be a rat tunnel.
Possess any rat that is near the tunnel and have it walk into the tunnel. While you are doing this you can also unlock the trophy Inhabitant, which requires you to stay in possession of others for “most of a 3 minute period”. To do so just stay in the tunnel for a full three minutes before exiting it and releasing the possession. While in the tunnel you will not be forced out of possession, which allows you to have the 3+ minute duration in one go.
To see a video of the method being performed, please view the video below: