For later patches, You need to "hook" the ws2_32.dll (or whatever it is that conquer uses for its networking) and when a "connect()" is called, catch it and replace it with your own connect function, so like change the IP and port.
Client starts up.
-> You login to any server
->Conquer calls connect() with an IP and port
->Attempts to connect
If you replace all the connect calls with your own, You can effectively make it login to your server.
You can do this using Detours, There's a thread in this forum where that whole thing is actually explained with help of Myself, Tane & Sparkie, Just put the pieces together and you have managed to copy and paste:)
Detours is currently only in C++.
For a C# Alternative there are libs out there to do this if you look into hooking that function in C#, I've found and used C# libs to accomplish this task.