NIT

The fees you filled first will be given back to you for that you have to follow a procedure that is distinct in every College. So, you can go the college and ask about it. Then, you will get your fees back.
Good luck.

You may have chance of getting seat in NIT please visit www.siksha.com/jeemaincollegepredictor.

Yes, you can apply but there are low chances for selection (If you are from general category). Hope for the best. You can surely apply. For applying to NIT you have to register yourself at JOSSA site. And fill up your respective NIT and branch you are interested in.

2018 MHRD Ranking of Engineering Colleges in India are mentioned at the link provided below:
https://www.shiksha.com/b-tech/articles/2018-mhrd-ranking-of-engineering-colleges-in-india-blogId-15711.

Cut-off for B.Arch at MNIT is as follows:-
250 for General, 220 for OBC, 160 for SC and 150 for ST. (These are approximate data)
So, it depends upon of which category you are.
Anyway participate in counseling till last round and believe in your luck a bit.
All the best!!

As per my idea, there are very few chances of getting admission in any NITs with obtained marks.You can predict your rank by following link:
https://www.shiksha.com/b-tech/resources/jee-mains-college-predictor

You have a very less chance of getting a seat in NIT.
But, you may have credibility of getting a seat into IIIT.

Since the margin between the cut-off and marks gained by you is only 1 (cutoff for ST is 24). Therefore, it is difficult that you will get the college:
https://www.shiksha.com/b-tech/resources/jee-mains-college-predictor
However, you can use the above link in predicting the college.
Best of luck.

Don't worry.
The fees for OBC category is a little bit lower than a general category. Also, you will get very good marks. Congratulations for it!
You will definitely get a college since the cut-off for OBC is just 45. You can appear for the scholarship exams and there are many schemes also for scholarship:
https://www.google.co.in/amp/s/www.shiksha.com/b-tech/articles/amp/nit-fee-structure-for-b-tech-2012-13-blogId-6033
I providing you the link. However, the link is of 2012-13 but don't worry, the fee will not differ more now. Best of luck.