It worked for my just adding the it to the ProjectFolder, and also add the folder programmatically like this.
var p = new Microsoft.Build.Evaluation.Project(@"C:\projects\BabDb\test\test.csproj");
p.AddItem("Folder", @"C:\projects\BabDb\test\test2");
p.AddItem("Compile", @"C:\projects\BabDb\test\test2\Class1.cs");
p.Save();