NATA and JEE MAINS  have got no connection. NATA is a test for students wanting to persue architecture as their career while JEE is for engineering and B.sc students. If you want to have a career in architecture and you have scored well in NATA you will obviously get admission in good colleges for architecture present in India. But it won't affect if you want a career in engineering . Only your JEE Mains mark will be taken into consideration .