- Hook the client
- Change certain data (Ex. prefix/suffix, cryptography keys, etc.)
- Have your server only rely on the changed data
Also make sure that your launcher will start the Conquer process with a specific flag, that's what TQ did with blacknull where Conquer would only start if it was called with that flag, which their auto-patch (launcher) did.
There are a few other techniques, but since you have to ask I guess you have no idea where to start.