If the access points cannot be in the same layer 2 network, they cannot be in the same cluster. If you have two clusters in different layer 2 networks, you will have to synchronize the changes betweeen them manually or obtain Airwave to do that for you automatically.
Devices in the same cluster do exchange broadcast traffic regularly, so you do not want to have a cluster separated by a WAN, even if you can somehow put them on the same layer 2 network.