DNS debacle, advice anyone?

So, a little background of my environment here. I have 30+ Xserves all running OS X server 10.5.5, 1 ODM, 6 T1 ODRs 10 T2 ODRs, and the rest are used for the Casper Suite as Netboot/imaging servers, distribution points, and file servers. We have two DNS names. An old name that is no longer used except for some PCs spread through out my place of work. The Macs (6,500+ clients and growing) are mainly in our 1:1 Macbook deployment and they mainly use the Wireless network for the most part, however I did notice that when building my directory some of the servers picked up the wrong DNS. So, the home folder mappings in WGM that pointed the right DNS we are suppose to use, didn't work. I have demoted/promoted several servers to get this fixed an am waiting for this school year to end so I can wipe it all clean and start over again. It seems that a lot of the older legacy devices still in place need this older DNS, and or DNS runs off of SLES Linux servers. So my question is, would it be wise to maybe chop it up in VLANs and assign DNS that way, Delete the mac servers out of the DNS entry that is for the legacy stuff in the DNS database, or what should I look into? I think the problem is I am pushing for a full DNS migration and while other system admins don't want to do that, so it may not happen. I know that some of the problems we have had in our network are due to funky DNS issues and they won't ever go away until we address them. Thoughts?