you have been defrauded by your brothers in connivance of the Branch manager. the, therefore, the complaint should be made against him too. he can try and prove his innocence once the case starts but afterward you cannot make him a party as that would be an afterthought and would look suspicious. also, your brothers couldn't have pulled off such a deal without the help of the BM.
you have to narrate the entire sequence of events as they happened. it is the job of the police to lodge FIR under relevant sections. when the matter goes to the court, your lawyer can move an application if the police have not investigated a particular aspect or not stated something which is of importance in the charge sheet.
yes the BM can be and should be named.