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The answer should be in the docs somewhere. Actually, you configure the two network links in the control domain and present them as vnets to the guests.
You then configure the first cluster to use these two links for the private interconnect. You should accept the default network address, but not the default netmask. Instead you should use the builtin functionality to limit the address space used by one cluster: limit the number of nodes, of interconnects and of zoneclusters. scinstall will then tell you how much of an address space starting with the default address is used by this cluster.
You then install the second cluster and do not accept the default interconnect address, but add up the network space used by the first cluster. Then you'll be fine.
To explain it by example. For the first cluster you chose 10.0.0.0 with netmask 255.255.0.0 for the interconnect. For the second you chose 10.1.0.0. with the same netmaks. It is now guaranteed that the interconnect traffic does not interfere.
Hope that helps