Some points in your query need clarification. As gathered from your query as it is, your company was to make a payment to a vendor of a certain sum but your partner has given the cheque with inflated amount deliberately which has bounced ?
First of all it is clarified that if the cheque has been issued by the company then if there is any liability your partner is equally liable in criminal case. So it can not be said that your partner has misused the cheque to your prejudice only. As far as action under section 138 NIA is concerned, primarily there are apparent lacunas and I suggest you hire a good advocate to look in to it.