I've spent a few days reading up and have managed to successfully (and fairly pain-lessly) setup Ubuntu Server 9.10. So far I have setup a clean install, installed OpenSSH and Squid and setup routing so that the Squid Caching is transparent to clients using the box as a gateway.
The server is setup with only one network card with 2 subnets, the system forwards requests on the HTTP port to the Squid port and provides a transparent cache. Requests coming in from either subnet pass through the server correctly however that is no isolation between the two networks.
Next I want to setup a 2nd network card and firewall between the two networks. I also want to setup Apache/PHP and serve an admin GUI for the system.
Step-by step configuration to follow....