test.cs

public static void SaveAnnotations(SmartDocument smartDocument) {

  using (TXTextControl.ServerTextControl tx = new TXTextControl.ServerTextControl()) {

    tx.Create();

    // load the SmartDocument PDF
    TXTextControl.LoadSettings loadSettings = new LoadSettings();
    tx.Load("App_Data/" + smartDocument.Name,
      TXTextControl.StreamType.AdobePDF,
      loadSettings);

    // find the original embedded document
    foreach (EmbeddedFile file in loadSettings.EmbeddedFiles) {

      if (file.FileName == "original.tx")
        smartDocument.Document = Convert.ToBase64String((byte[])file.Data);

    }

    // load the original document
    tx.Load(Convert.FromBase64String(smartDocument.Document),
      BinaryStreamType.InternalUnicodeFormat);

    // create an attachment for the original document
    EmbeddedFile efOriginal = new EmbeddedFile("original.tx",
      Convert.FromBase64String(smartDocument.Document),
      null);
    efOriginal.Relationship = "Source";

    // create an attachment for the annotations
    EmbeddedFile efAnnotations = new EmbeddedFile("annotations.json",
      Encoding.UTF8.GetBytes(smartDocument.Annotations),
      null);
    efAnnotations.Relationship = "Source";

    // attach the files
    TXTextControl.SaveSettings saveSettings = new TXTextControl.SaveSettings() {
      EmbeddedFiles = new EmbeddedFile[] { efOriginal, efAnnotations }
    };

    // save the SmartDocument as PDF with attachments
    tx.Save("App_Data/" + smartDocument.Name, 
      TXTextControl.StreamType.AdobePDF, 
      saveSettings);
  }
}