Try using the system.IO.Packaging namespace

Quick example for replacing the Data with a data.xml file

//Load in the XML

XmlDataDocument myXmlDocument = new XmlDataDocument();

myXmlDocument.Load(dataPath + "\\data.xml");

//Open the File using the packaging API

using (Package p = Package.Open(createdDocPath, FileMode.Open, FileAccess.ReadWrite))

{

   Uri partUri = new Uri("/CustomXml/item1.xml", UriKind.Relative);

   PackagePart part = p.GetPart(partUri);

   //Overwrite the part with the new XML

   using (Stream s = part.GetStream(FileMode.Create))

   {

      myXmlDocument.Save(s);

   }

   p.Flush();

}