Did you get the e-challan from site? I wasn't getting it. If you get it, then take a cheque,fill the required amount and go to the bank and submit the cheque along with challan. Get all the 3 copies of challan stamped(most important) by the bank and as far as I know, you would only be given the student's copy. Bank would keep the institute's copy and Bank copy.
And you need not pay it today necessarily. Just pay it before reaching out to RC