I am trying to configure two Kubernetes cluster on bare metal ubuntu that shares the same ETCD cluster, I have no idea where to do the changes to it work.
You should be able to configure the etcd instance(s) used by Kubernetes using the --etcd_servers flag on the kube-apiserver component. It also has a flag for specifying the prefix to put all of its objects under in etcd.
However, we typically recommend using a dedicated etcd instance for Kubernetes anyway so that it can't be affected by other users of the etcd cluster.
Agreed with Alex, please don't forget to configure flannel to use your existing etcd cluster, it is also relying on etcd to work.