Hey! If the percentage of qualifying exam has been asked and you have been alloted college on the basis of JEE Mains 2019 score then you should fill the JEE Mains 2019 percentile. Don't worry much about the same as the details is to be filled in the hostel admission form. Hope this may help you. 

Hi Aspirant,

I think by qualifying marks it means the percentage you got in Intermediate not the JEE Mains in particular. You can leave that option balnk and ask it on the spot and fill it, it should not be that big of a deal. It won't take much time. So if you are still confused, fill it there itself after confirming.

Good Luck !!