Once the buyer intents to register agreement of sale, he/she have to make a pay order of the stamp duty amount in the name of the respective body, depending on the jurisdiction where the property is situated. The pay order is then given for the franking of the agreement and is later duly signed by both the parties (ie buyers and sellers)
As far as I know buyer would be liable to pay stamp duty of flat 6% on the property price. Stamp Duty has to be against every agreement for sale that needs to be registered. Without the same the registration process will not be complete.