Currently, most of the work is done online only but yes eventually you will have to use cash (if you want) for all the payments. For example, when you pay for the JoSSA counseling (which includes INR 44,000 towards the institute and INR 1,000 towards the counseling fee) you will have to make DD with the cash.
The college will automatically withdraw the semester fee from the 2nd semester onwards. The mess fee from 3rd semester onwards you can pay through credit cards or debit cards.