Just unpack the stuff in your conquer folder.
First you need to edit your server.dat file so that the server ip of the server you use points to 127.0.0.1
Then, you need (if you are on one of the newer servers, put the original ip address of your server into qoproxy.ini at the line remoteloginip=69.59.142.13 (<-- that's the ip of the old servers, which is default)
Then just start to batch file and you'll see a startup notice. Then run Conquer (or later on Cotobo when it's fixed) as you usual do and login into your server. You'll see debug output messages in the command line window if it's correct working.
For the ppl who are screaming this will spoil the game... It also would if just a few have it. It just equals the chances. But don't get me wrong, I'd rather also see this fixed, but as long as it is not, I think it's a bit silly to think just the "elite" are allowed to have it. What makes you more special than any other who would use it?