Yes, of course. The counselling process includes choice filling which means where you have to filled all the colleges and branches you want in a proper order. Even after getting good score and rank, many students fail in choice filling properly. You can choose more than one college and more than one branch in Wbjee counselling. In WBJEE Counselling, there is no such provision that you have to choose only one college. The choices you fill in WBJEE counselling, would be based on your interest. If you choose CSE in ABC college, then you can choose CSE in PQR College or can choose ECE or any other branch in ABC College. Let me give you an example, you'll understand it better. So let's think, you have selected Computer Science and Engineering in suppose Institute of Engineering and Management as your first option. Then your second choice can be, CSE in any other college suppose Techno India Salt Lake or can be Electronics or any other branch in IEM. During choice filing, you must put top colleges in the top of the list followed by average engineering colleges. You can also go through this link
http://engineering.careers360.com/articles/wbjee-counselling