1. the jurisdiction of the cheque bounce case will be the place where the cheque was presented for the encashment (company's place)
2. you should reply the legal notice under section 138 of NI act as the non-reply would make up a presumption that you admitted the amount claimed in the legal notice
the mail, intimation regarding the damaged goods, mentioning of the cheque as a security will help you to counter the case, however, for an near to exact opinion, a bare look on relevant documents is necessary