The mechanical city of Sotha Sil is controlled from its highest tower - the Kogitum Centralis, where Lord Seth himself puts on a special helmet (similar to a virtual reality helmet), puts his hands on two control panels - and so he can change, rebuild and control any part of his city or all of them at once.
This was used by the mistress Nocturnal, who tried to "hack" the Sotha Sil connected to the helmet with the help of the Skeleton Key - her own very powerful Daedric artifact, which is subject to any locks, doors and...even minds. City was created as a functional copy of Nirn, and Nocturnal wanted to gain control of the Clockwork City and, accordingly, have access and influence in Nirn as well. We can only guess how much power she would receive if her plan will be finished.