Could I fill two branches separately in one NIT in josaa counselling with other choices. As one choice down down to triple IIIT and other up
Yes, You can. In JoSAA you can fill any number of Choices. Suppose First you want to fill NIT Jaipur CSE, then NIT Delhi CSE and later NIT Jaipur Mechanical. Each course in each NIT is considered as Choice and You can fill it in any order they all are independent.