The basic difference is that once JoSAA completes its process of admissions for IITs, NITs and other colleges, CSAB conducts some special rounds(generally 2 rounds) to fill up the vacant seats of NITs, IIITs and other colleges (not for IITs). 

Eligibility for CSAB special rounds:

1. All the candidates who are eligible for JoSAA counselling are equally eligible for CSAB. 

2. If you are not allotted any seat via JoSAA then you can switch for CSAB. 

3. Even if you are holding a seat, then also you can apply for CSAB special rounds. (There might be chances to secure better branch). 

So,yes you can get the seat that you want as your choice.

Hope this will help you.