@rider: Wtf? Why do you need to make 2 MySQL processes? You don't need to run 2 MySQL servers, so the port stays as 3306...one MySQL server can handle the load if properly maintained.
@OP/becko: You need to edit the Auth & Game port of the second server (like 9959 & 9866..as an example).
You may have multiple IPs, but you still have one server/computer.