I've seen a lot of guides saying that it is impossible to run and allow people to connect to both Arc Emu and Mangos off the same machine. This is completely false!!! You can even use the same realmlist if you want. Here is the secret.
Step 1: Open up the configuration sheet for arc emu which contains the realm information. Make sure the realm port is not the same as the realm list port for the Mangos server. It doesn't matter which is which just as long as they are different.
Step 2: Close and save the document. Start whichever server you want first. This also does not matter. Start Mangos or Arc Emu first, either way it doesn't matter. Whichever one you started first is the one that your players will connect to automatically when putting in your default realmlist.
Step 3: Say your realm list is armageddonwow.no-ip.biz. When your players use this as their realm list, they will either access the Arc Emu server or Mangos server depending on which you started first. If you wish for your players to access the other server, have them type in the realm list and then a ':' symbol and then the port ID number after. This will forward the players to whichever realm the port corresponds to.
Step 4: To avoid conflicts of realms, have your players always use the port ID number after which corresponds to the server they wish to play on. Should the player wish to access arc emu/mangos, all they have to do is put the ':' and the port ID number after the realmlist. This would look something like
'set realmlist armageddonwow.no-ip.biz:1991'.
Step 5: That's it! It's simple and it works if the ports are different for each realm. Good luck and I hope I helped.