dog is correct, you can set it up like this:
Network CP
NIC1->IPX->NetWare Client
NIC2->IP->Microsoft Client
That way, traffic from each protocol will only go out its respective NIC.
The BIG drawback to this is the harebrained way certain M$ OS's deal with any change to the Network settings.
After carefully "tuning" a PC's Network settings, the OS will at times bind every available protocol to every available adapter and every available client. Only certain operations do this, but it took me FOREVER to get my techs straight on checking and double-checking this.
Which brings me to my peeve about your setup (don't get me wrong, this isn't directed at you, but rather, at your doofus IT clerics):
Except in *very* RARE circumstances, no client PC should ever need 2 NICs. The beauty of networking is that it allows you to send whatever the hell protocol you want, whenever you want, wherever you have the proper infrastructure. Because protocols are largely transparent, at least from layers 3 on down (of course, not completely transparent, as spidey, ScottMac, L3, and others will be likely to say....but don't stop me guys, I'm on a roll), the proper place for management of multi-protocol data transmission should be handled in the wiring closet by the infrastructure, not at end-user dektops.
Let me back up by saying...I never like to pass judgement on anyone else's network (mainly 'cause I hate it when someone tries to tell me about MY networks without knowing anything about them), and I don't know the whole story with your company's setup, but it sounds to me like your IT group is spending double the money (by duplicating networking hardware) with no increase in functionality.
I don't see the logic in a "too much traffic" argument. If there is too much contention for not enough bandwidth, then look at policy-based networking or an infrastructure upgrade, rather than pay for "another" network that will inevitably be filled up, usually more sooner than later.
If they are worried about "chatty" IPX broadcasts flying over their WAN links or some such nonsense, they ought to be fired. "Spoofing" broadcasts and configuring lists of services and resources have been around since the good old days of NetWare 3 (1986 anyone?) And if they violated standard design practice...aw hell, gonna quit 'cause nothing pisses me off more than IT stupidity. We have a tough enough time getting folks to take us seriously without all the Dilbert and Nick Burns wannabes