IIT Dhanbad (ISM) - Indian Institute of Technology (ISM)

UPES rank is 3rd in terms of petroleum engineering. 1st is IIT, Bombay and 2nd ISM, Dhanbad.
You can check the ranking here –
http://www.indiaeducation.net/careercenter/engineering/petroleumengineering/

An IIT will always have its brand value. BITS, Pilani too has its own advantages. Go with it.

For choosing the branch, go with the one that interests you. CS and civil are two absolutely different streams that cannot be compared in terms of education. Both are IITs so equally good. Decide and flourish.

For UG courses (Engg.), it is through IIT-JEE. For PG courses, M.Tech, it is done through GATE and for MBA through CAT score.

Check the official website www.iitism.ac.in for the lists and various other notifications.

It would depend on what you further aspire. You can take higher studies like M.Tech in various fields or branches in petroleum, or take up management courses like full-time MBA or executive MBA or so.

As ISM-Dhanbad is now IIT-Dhanbad, it is better than BIT Mesra.

No, ISM-Dhanbad does not take students through WBJEE.

ISM, Dhanbad is a better choice than MI, Pune.

The total course fees for the MBA program including mess and hostel charges would be around Rs 4 - 5lakhs. This is subjected to change. As there is revised fees structure.
For the marks, I am sorry, but I don't have information. It is purely done by our administration, and they don't share such information with students. All the best!