I have secured AIR 2239 in jee advance 2016 general. What should be the order I fill up is JOSAA. I dont want a research based branch. I have also lceared bitsat with a score of 403 n im sure to get cse there. My personal interest is in cse n im not getting cse in any core IIT. Would it be right to choose bits pilani cse over any thirdclass branch at the IITs?

Go with your interest. Because if you have interest then you will do your best and best is selected by the company. In the meanwhile you can also check for some Private Universities. There are some Private Universities which are equally good. They provide good Infrastructure, Faculty and Placements.You should choose a college which give you opportunity to work in live projects and give you good exposure. You may browse some web sites and check their details like Lovely Professional University, Nirma University, Noida International University etc...