Itr

one of my clinet is running school, under educational society, now the department issue letter to file return, because exceeding 10L deposits in banking company, my how to file return, i did not register 12A, PLEASE what i will do in this regard, can file itr, which itr used, how do we pay tax, my opinion is 1 croe does not exeed so that need not file it return, please guide to us