Am I right in thinking that your setup is like this?
Internet --> Router --> Linux Box --< Rest of network
If so, then you will want your Linux box configured so that eth0 is on one ip group and eth1 is on another, you would then set your Windows boxes to connect via (proxy?) your Linux box's eth1 ip address. Lots of people will suggest that you use dhcp for the internal, local network (of with your Linux box's eth1 will be a part of), but I maintain that if you're on a very small network (< 10 machines), it is just a easy to maintain if you give each one a seperate IP address.