Well, with VMWare Server 2.0 you can go into Host and configure the virtual networking setup for the 2 NIC's. This way your server can have 2 NIC's configured and these 2 networks can be assigned to any of the virtual machines.
The problem you will have is when you try to add the 2 NIC's to the same VM...Windows is going to complain if you try to setup a default gateway for both network cards since the box shouldn't have 2 default gateways.
Typically, you use the 2 NIC setup when you want 1 VM to participate in 1 VLAN, while another VM participates in another VLAN.