After getting Challan, you will submit the challan with SBI Tis Hazari Delhi,Branch, there after Revenue Department will issue a verification letter for challan and he will invite you for meeting, there after he will issue a stamping certificate.
You can pay the stamp duty electronically, but you have to deposit the required amount at the designated branches of CBI, BOB, PNB, ETC, on deposit of required amount they will issue a stamp certificate which is required to be deposited at the stamp department, than they will verify your certificate online and thereafter issue stamp duty payment certificate accordingly.
for deposit of amount to bank download the deposit challan at http://www.shcilestamp.com/Application_Ind.pdf