Well since your hosting the Unreal Tournament servers and web sites on the same box, it really will not matter if you connect to the servers through an IP shared with the web servers. You wont notice lag through the internet connection. (Assuming your on a fast 10Mbit+ connection) The only lag you may get would be from the server itself, but just so long as it's a newer server with plenty of RAM, you'll have no problems.
As for running multiple servers on the same box. There are many ways in doing this.
You can create a new account for each server or run the server under the same account.
If you use the same account, then it's best to have multiple directories with the servers placed in each. ut1, ut2, ut3 or something. Then start each one individually.
If you use multiple accounts, then well. That should be self explanatory.
To make things easier though, if your the only one running the servers then set them all up under the same account, so when you need to do something to the server(s) you only have to log into one account to do whatever it is you want to do.
You can also run multiple servers under the same directory, but SOME mutators/mods will not work correctly. Mostly these are the ones that require a seperate ini file that can't be defined in the script by the user. If you don't run such mods, then you just need to start the server with a script and have multiple server.ini files to handle each individual server. Not recommended, as problems may occur.
I do recommend setting up
http://ut.abfackeln.com/asu.html for the servers though, as it can make installing mods, starting/restarting/stoping the server, setting up the configuration, ect... much easier.
If you want to have dm.domain.net to be the host for the servers, then just make sure that dm.domain.net is pointed to the right IP. The only problem with this would be when you run multiple servers on the same IP, you'll need different ports. So it may have to be something like dm.domain.net:9988 or whatever ports you choose.
In the server ini file for each server you'll have to define the IP and Port the server(s) will use. If you use one IP for all the servers, you'll HAVE to define different ports for each. This includes the game port and web admin port if you choose to use that. If you are just going to use the 3 IPs, then make sure you assign the IPs to each server manually.