var signature = signedXml.GetXml();
xmlDoc.DocumentElement.AppendChild(signature);
var data = xmlDoc.DocumentElement.SelectSingleNode("/root/node");
signature.AppendChild(data);

static void Main()
{
  SignXml(@"
  <MyFile xmlns=''>
    <Object Id='Settings'>
      <ProductID>P2</ProductID>
      <FirstName>John</FirstName>
      <LastName>Jackson</LastName>
    </Object>
  </MyFile>", Certificate, @"D:\Trash\1.xml");
  var xd = new XmlDocument();
  xd.Load(@"D:\Trash\1.xml");
  var checker = new SignedXml(xd);
  // сигнатура - последний дочерний элемент корня
  var signature = (XmlElement)xd.SelectSingleNode("/*/*[last()]");
  checker.LoadXml(signature);
  var res = checker.CheckSignature(Certificate.PrivateKey);
  Console.WriteLine(res);
  Console.ReadKey(true);
}

static X509Certificate2 Certificate
{
  get
  {
    var keyStore = new X509Store(StoreName.My, StoreLocation.CurrentUser);
    keyStore.Open(OpenFlags.OpenExistingOnly | OpenFlags.ReadWrite);
    return keyStore.Certificates.Find(
      X509FindType.FindBySubjectDistinguishedName,
      "CN=MyCertificate", false
      ).Cast<X509Certificate2>().FirstOrDefault(
        c => !string.IsNullOrEmpty(c.Thumbprint) &&
        c.HasPrivateKey &&
        c.NotAfter > DateTime.Now &&
        c.NotBefore < DateTime.Now);
  }
}

static void SignXml(string content, X509Certificate2 certificate, string filePath)
{
  var xd = new XmlDocument();
  xd.LoadXml(content);
  var sx = new SignedXml(xd) { SigningKey = certificate.PrivateKey };
  var @ref = new Reference { Uri = string.Empty };
  @ref.AddTransform(new XmlDsigEnvelopedSignatureTransform());
  sx.AddReference(@ref);
  var keyInfo = new KeyInfo();
  var keyData = new KeyInfoX509Data(certificate);
  keyInfo.AddClause(keyData);
  sx.KeyInfo = keyInfo;
  sx.ComputeSignature();
  var signature = sx.GetXml();
  // сигнатура будет последним дочерним элементом корня
  xd.DocumentElement.AppendChild(signature);
  using (var fs = new FileStream(filePath, FileMode.Create))
  using (var xw = XmlWriter.Create(fs, new XmlWriterSettings { Indent = true }))
    xd.Save(xw);
}

<?xml version="1.0" encoding="utf-8"?>
<MyFile xmlns="">
  <Object Id="Settings">
    <ProductID>P2</ProductID>
    <FirstName>John</FirstName>
    <LastName>Jackson</LastName>
  </Object>
  <Signature xmlns="http://www.w3.org/2000/09/xmldsig#">
    <SignedInfo>
      <CanonicalizationMethod Algorithm="http://www.w3.org/TR/2001/REC-xml-c14n-20010315" />
      <SignatureMethod Algorithm="http://www.w3.org/2000/09/xmldsig#rsa-sha1" />
      <Reference URI="">
        <Transforms>
          <Transform Algorithm="http://www.w3.org/2000/09/xmldsig#enveloped-signature" />
        </Transforms>
        <DigestMethod Algorithm="http://www.w3.org/2000/09/xmldsig#sha1" />
        <DigestValue>evQM25ma3WGkWkNic0d1g+XiVws=</DigestValue>
      </Reference>
    </SignedInfo>
    <SignatureValue>B9EcIp/chKi........................wJzuxtF4Gre0o=</SignatureValue>
    <KeyInfo>
      <X509Data>
        <X509Certificate>MIIB6TC..........................V/hE6sbFofg==</X509Certificate>
      </X509Data>
    </KeyInfo>
  </Signature>
</MyFile>

var xnm = new XmlNamespaceManager(xd.NameTable);
xnm.AddNamespace("ds", "http://www.w3.org/2000/09/xmldsig#");
var signature = (XmlElement)xmlDoc.SelectSingleNode("/*/ds:Signature", xnm);

<Reference URI="#AuthorizedSettings">

var xmlDoc = new XmlDocument();
xmlDoc.LoadXml(content);
var signedXml = new SignedXml(xmlDoc) { SigningKey = certificate.PrivateKey };
var @ref = new Reference { Uri = "#AuthorizedSettings" }; // следим, чтобы id подписываемой ноды соответствовало URI
@ref.AddTransform(new XmlDsigEnvelopedSignatureTransform());
signedXml.AddReference(@ref);
var keyInfo = new KeyInfo();
var keyData = new KeyInfoX509Data(certificate);
keyInfo.AddClause(keyData);
signedXml.KeyInfo = keyInfo;
signedXml.ComputeSignature();
var signature = signedXml.GetXml();
// Ноду <Object Id='Settings'> помещаем внутрь сигнатуры
signature.AppendChild(xmlDoc.DocumentElement.ChildNodes[0]);
// Сигнатуру помещаем в документ
xmlDoc.DocumentElement.AppendChild(signature);
using (var fs = new FileStream(filePath, FileMode.Create))
using (var xw = XmlWriter.Create(fs, new XmlWriterSettings { Indent = true }))
  xmlDoc.Save(xw);

var xmlDoc = new XmlDocument();
xmlDoc.Load(@"....");
var signedXml = new SignedXml(xmlDoc);
var signature = (XmlElement)xmlDoc.DocumentElement.ChildNodes[0];
signedXml.LoadXml(signature);
var res = signedXml.CheckSignature(Certificate.PrivateKey);

<Signature xmlns="http://www.w3.org/2000/09/xmldsig#">

<MyFile xmlns="">
  <Object Id="Settings">
    <ProductID>P2</ProductID>
    <FirstName>John</FirstName>
    <LastName>Jackson</LastName>
  </Object>
</MyFile>

static void SignXmlWithEnvelope(string content, X509Certificate2 certificate, string filePath)
{
  var xmlDoc = new XmlDocument();
  xmlDoc.LoadXml(content);
  var signedXml = new SignedXml(xmlDoc) { SigningKey = certificate.PrivateKey };
  var @ref = new Reference { Uri = @"#Settings" };
  @ref.AddTransform(new XmlDsigEnvelopedSignatureTransform());
  signedXml.AddReference(@ref);
  var keyInfo = new KeyInfo();
  var keyData = new KeyInfoX509Data(certificate);
  keyInfo.AddClause(keyData);
  signedXml.KeyInfo = keyInfo;
  signedXml.ComputeSignature();
  var signature = signedXml.GetXml();
  signature.AppendChild(xmlDoc.DocumentElement.ChildNodes[0]);
  xmlDoc.DocumentElement.AppendChild(signature);
  using (var fs = new FileStream(filePath, FileMode.Create))
  using (var xw = XmlWriter.Create(fs, new XmlWriterSettings { Indent = true }))
    xmlDoc.Save(xw);
}

static X509Certificate2 Certificate
{
  get
  {
    .....
  }
}

SignXmlWithEnvelope(@"
  <MyFile xmlns=''>
    <Object Id='Settings'>
      <ProductID>P2</ProductID>
      <FirstName>John</FirstName>
      <LastName>Jackson</LastName>
    </Object>
  </MyFile>",
  Certificate, @"D:\Trash\1.xml");

<?xml version="1.0" encoding="utf-8"?>
<MyFile xmlns="">
  <Signature xmlns="http://www.w3.org/2000/09/xmldsig#">
    <SignedInfo>
      <CanonicalizationMethod Algorithm="http://www.w3.org/TR/2001/REC-xml-c14n-20010315" />
      <SignatureMethod Algorithm="http://www.w3.org/2000/09/xmldsig#rsa-sha1" />
      <Reference URI="#Settings">
        <Transforms>
          <Transform Algorithm="http://www.w3.org/2000/09/xmldsig#enveloped-signature" />
        </Transforms>
        <DigestMethod Algorithm="http://www.w3.org/2000/09/xmldsig#sha1" />
        <DigestValue>JcVPQRoHH4kpasAvbTA1NEw52bw=</DigestValue>
      </Reference>
    </SignedInfo>
    <SignatureValue>gLsig1m+n/bEJJDLsqJ..........CMOE=</SignatureValue>
    <KeyInfo>
      <X509Data>
        <X509Certificate>MIIB6TCCAVagAw........sbFofg==</X509Certificate>
      </X509Data>
    </KeyInfo>
    <Object Id="Settings" xmlns="">
      <ProductID>P2</ProductID>
      <FirstName>John</FirstName>
      <LastName>Jackson</LastName>
    </Object>
  </Signature>
</MyFile>

var xmlDoc = new XmlDocument();
xmlDoc.Load(@"D:\Trash\1.xml");
var signedXml = new SignedXml(xmlDoc);
var xnm = new XmlNamespaceManager(xmlDoc.NameTable);
xnm.AddNamespace("dsig", "http://www.w3.org/2000/09/xmldsig#");
var signature = (XmlElement) xmlDoc.SelectSingleNode("//dsig:Signature", xnm);
signedXml.LoadXml(signature);
var res = signedXml.CheckSignature(Certificate.PrivateKey);
Console.WriteLine(res);

var sx = new SignedXml(xmlDoc) { SigningKey = certificate.PrivateKey };
sx.Signature.Id = "1";

var @ref = new Reference { Uri = string.Empty };
@ref.AddTransform(new XmlDsigEnvelopedSignatureTransform());
@ref.AddTransform(new XmlDsigC14NWithCommentsTransform());