You can prepay but only till outstanding amount is showing and it is not zero. I just tried when outstanding amt. was 1951, I paid 5K and it shown successful but not settled. Maybe it will get reversed. Will let you know whatever happens in next 3 days.
I never got the option to enable AutoPay in BillPay tab for any credit card in HDFC BillPay external site. There is also smartpay option in credit card section with similar benefits although never tried it but it may allow payment via NB and DC. On electricity and other types I do get auto-pay enabling option by turning it on but not on CC in HDFC Billpay where it remains faded. You can select DC of your choice while setting up.
IMHO, avoid auto-pay as full bill is presented and if less amount is there in limits it may reject payment as may be some banks deny lesser payment than bill presented. Sometimes we forget to keep enough bank balance to let it go through and it charges for failed mandates. Though we can set the amount to be paid but it has more hassles than paying manually. Just my view as I keep myself away from ECS, DC Mandates/Auto-Pay things. Don't save my cards either on any site.
Have maintained excel month-wise for all payments of me and family members. So all dues of taxes, insurance policies (life, general etc.) are there in 12 different sheet named Jan to Dec in single excel sheet. On a Sunday I went through them to clear things. Most of payments for me are in Oct-Dec quarter except CC bills which are every month work.