In the current release of IAP SW you cannot do this. In order to have two separate clusters management traffic must be in two separate Vlans so the IAPs in Cluster 1 cannot see, and join Cluster 2.
In the next major release, 4.1, we will be introducing an ap-group feature that will allow all IAPs to be in one cluster while alowing certain IAPs to advertise one SSID and others to advertise a different SSID. This is still, however, 4 - 8 weeks away.
In the meantime, separate them by vlan. You could put one IAP in "standalone mode" and it will not join a cluster and you will manage it independently.