tennebrew is right, revolt then cs.
first you have to clear the city (which i think you've already done)
second, send a specially designated revolt attack (all clearing attacks can be sent as revolt)
third, the revolt will last 12 hours. during this time, the defend has control of the city hand can continue to build building and troops and move in support. you can continue to send clearing waves during this time. keep in mind other players can land revolt attacks during the same interval and then move on to the next steps. it's important to keep an eye on the city and know what is happening.
fourth, a second 12 hour period starts (hours 12-24) when you must land your cs. make sure you time clearing waves to arrive before the cs in case any support has arrived. due to distance or slow tt, don't forget to send you cs before the revolt attack if necessary.
fifth, the moment you cs lands, you have conquered the city