Almost. I figured out that you must first create a folder called 'Published' in the 'CookedPC' folder. Right click on the 'Published' folder, and add a new folder called 'CustomMaps'
There are a few ways for the maps to work, you can either put all the files in the CustomMaps folder, or make new folder within the CustomMaps folder with the name of the map.
After that, make sure you put the Map.ini file in the UTConfig folder with all the other .ini's. The final step is adding the map to the maps cycled list.
It's a pain in the neck at the moment to add custom files to your server, but what can ya do. Hopefully this is fixed in the near future.