I don't believe you can do split DNS with a single 2003 instance. If you have one instance on each network segment, you can set the inside to answer the zone and to forward all other queries to the new DNS server.
The Microsoft DNS server allows you to bind it to a specific interface, but not to run two different services with split data. Since you can unbind it from an interface, there may be a way to run ISC Bind on that other interface. This would have you running Microsoft DNS service on one interface and BIND on another, or potentially bind on both.
The easiest ( if klunky ) way to do it within the Micosoft ecosystem would be to run the 2003's in Hyper-Vs as virtuals each with it's own DNS server and data. They could still be in the same domain if you create the DNS zones as not active directory integrated. Server 2008r2 would let you run as an evaluation and give you time to migrate. Server 2012 activates immediately. Be sure to check out the licensing on Server 2012 in Hyper-V. You can run several instances on Standard and 'unlimited' on the Datacenter license.