Aroon,
The RFS6000 can be upgraded only to as high as 5.8.5 (you're currently running 5.8.4)
The NX5500 can run all the way to the latest WiNG code version - 5.9.6
As you seem to already recognize, you cannot run the older model APs with the newer 5.9.x code...so you have them adopted and managed by the RFS6000.
Regarding combining these two controllers into a 'cluster' - No, cluster formation requires that the two controllers be the same model as well as be running the same firmware version. In your case, there's no way to make this happen (even though you could load 5.8.4 onto the NX5500, the two controllers are very different hardware models).
As a side note though, running both of these systems on the same VLAN (and if the APs exist within the same RF environment) will create some challenges that I feel are beyond the scope of being covered here. I would very much suggest reaching out to GTAC to discuss this deployment with someone.