The 2 systems will always act as 2 independent systems, even on failover. On failover the remaining controller will run a virtual version of the failed filer, and it will keep the majority of it's personality, including it's AD membership, and any DNS configuration should stay active. However, I'd probably recommend putting all DNS servers, for both networks, into each system, just in different order depending on that systems priority. Ideall you want both the filers to be able to find eachother, even if they are on different networks.
From a failover point of view, make sure that all networks are presented to both the filers so that they can failover without network disruption. You could do this with named failover interfaces, or just present all the VLANs and let the filer do the VLAN configuration on their own interfaces.
Definitely worth running a few failover tests before going live to make sure all the network configuration is correct and won't cause an issue though.
Re: active/active configuration with different dns
I have one more question I have 2 controllers with 3 disk shelves with 24disk drives 300GB. one controller owns 1 disk shelf and other controller owns 2 disk shelf's. from first disk shelf I need one big aggregate using all the disk drives(one spare) in the disk shelf . how should I configure raid groups .