See according to the information I can muster, what I found is that there is no mention of GATE Marks anywhere during the filling of application form.  Everywhere it is mentioned as GATE score itself . So I would say that don't worry as far I have check you are in the clear and you have filled the right thing

Hello,

See if during the last registration form if they wanted the gate marks,then you should have entered gate marks only,the form which was submitted at the last might have more importance than the one which was submitted preeviously.

So now if you have submitted it,then you can wait for its latest/upcoming update.

If there is an option of rechanging the details,then you can enter the 'gate marks'.

Otherwise if there is any confusion or misconception during their process,you can contact the concerned officials/authorities.

Hope it helps!

ThankYou!

Regards!

Shikhar Singh Chauhan