Mohammed,
Generally, you can think of federation as a way to centrally track and manage your multiple clusters. More of a way to run single 'sreport' and 'sacct' commands. There are added abilities such as being able to specify the cluster to send a job to, but for all intents and purposes, the clusters themselves are independent.
It sounds like what you may want is multiple partitions in the same cluster. You can have 2 that comprise of the sets of nodes and a third that is comprised of all nodes. Or a single partition with all nodes and have features that delineate what node can do what (a node-locked license, for example). Then you can send a job to a specific subset of nodes.
Quite a few other ways to design the ability you describe, but separate clusters is not one of them.
Brian Andrus