Instructions:
1) Make a copy of your MatchServer folder and rename it to ClanServer.
2) Delete MatchServer.exe, place ClansServer.exe in the folder.
3) Rename port.txt to por2.txt.
4) In por2.txt, change both "6000" to "6005".
5) In server.ini, make it look like this:
Edit the UserID, pass, and your IP part then save.
6) Goto SSMSE(SQL Server Management Studio Express), open the table "dbo.ServerStatus", make a new one with the ServerID = 2, Port = 6005, and Type = 3. For the IP, change it to your WAN or Hamachi IP.
Example:
Open ClansServer.exe and MatchServer.exe and wala! You have 2 servers running.
Proof:
Some credits to Demantor! Don't ask why. :P