stamp duty & charges

I have booked one flat.  In that payment term, black & white component is there.

I have been told by the builder to pay first black amount alongwith stamp duty &registration charges (to the builder only). He will do all the procedures related to stamp duty and registration charges.  He is doing for all the flats.

I would like to know is it safe or should i do it personally?  If i want to do it personally, when i have to go for stamp duty and registration and what are the documents which i need to submit?

Shall i get the agreement paper after paying the black amount?

Pl. clarify so that i can take proper step.

Sowmya