21 September 2017
Pay by creating a challan. Make payment under respective head of CGST, SGST & IGST. No difference between Regular payment and RCM payment. After payment amount will get credited in Electronic Cash Ledger then you can offset the liability in GSTR3B.
21 September 2017
Mr Anshu you being a RD and recipient of goods is liable to pay GSt on freight under RCM. If transporter has charged you tax, he is not authorised to collect tax from you. It is you who is to pay under RCM.