As much as it's clearly stated in the letter sent to you from LVO. that you are expected to pay your RPRF. with Bank Draft/Cheque. I still think you can raise CSE. inquiries and tagged it Urgent to take permission from LVO. to pay the fee online. If you check FSW 2013 thread, many people have paid it online to LVO. and they did not have any problem but you have to remember that they applied on FSW while you applied on PNP.
Having said that, if i were you, i will make the payment with Bank Draft/Cheque as early as possible.
Wish you best of lucky in the journey ahead. 8)