I sign PDF documents using 5.5 version of iTextSharp. Below is the sample code.
// Set the reader (PdfReader) and output (Stream) first
PdfStamper stamper = PdfStamper.CreateSignature(reader, output, '\0');
PdfSignatureAppearance signatureAppearance = stamper.SignatureAppearance;
signatureAppearance.SignatureRenderingMode = PdfSignatureAppearance.RenderingMode.GRAPHIC_AND_DESCRIPTION;
signatureAppearance.Reason = "I love signing";
signatureAppearance.LocationCaption = "";
signatureAppearance.SignatureGraphic = Image.GetInstance(this.imageFolderPath + "sign.png");
signatureAppearance.SetVisibleSignature(
new Rectangle(100, 100, 300, 200),
reader.NumberOfPages,
"Signature");
// Get certificate from store, here I am reading file
X509Certificate2 cert = new X509Certificate2(certFile, certPassword);
var keyPair = DotNetUtils.GetKeyPair(cert.PrivateKey).Private;
BcX509.X509Certificate bcCert = DotNetUtils.FromX509Certificate(cert);
var chain = new List<BcX509.X509Certificate> { bcCert };
IExternalSignature signature = new PrivateKeySignature(keyPair, "SHA-256");
MakeSignature.SignDetached(signatureAppearance, signature, chain, null, null, null, 0, CryptoStandard.CMS);
stamper.Close();