Open DataPath.cs, and where it is written: private static string CustomPath = null;
Enter the directory path to your UO game installation folder like private static string CustomPath = @"C:\runuo\client";
You should see a list of files in that DataPath.cs file as well, and should create a new directory somewhere (like in above) and copy the files listed in DataPath.cs from your UO folder, to this new one. The new folder would be the directory you enter in the above line.
That is what m309 meant about having a second folder of files for the server to run on.