There is a small catch since accused signed the cheque on behalf of the firm, under such circumstances the proprietor must have given some authority letter to the Bank to give this power to some one else (that is accused).
S.141 clearly not applicable to proprietorship firms, there are many orders on these lines, please see the Andhra High Court order in "Dr. V. Bala Raju vs 1.M/S Pashak Feeds Pvt Ltd., on 1 October, 2004" if this can be of any help.
You may have to refer to The Indian Contract Act also, which makes the granter liable for the acts of agent, so ideally above ruling coupled with the Indian Contract Act, rules out accusation to non proprietor signatory of the cheque.
But other party can argue that Bank account is managed by the accused, on behalf of proprietor, you can cite above two and also the fact that account is infact managed by accused but it is not his account and prop should be solely responsible for the same as vicarious liability does not come into picture. Your case would have been simple if he was just managing the affairs, signing the cheque is more than that.
There are few orders in which proprietorship firm is removed from the accused as being no legal entity, so ideally only proprietor should be the accused, the name of agent or manager comes only after non juristic accused. These are few argument lines which may support you, approach HC under S.482, as I am afraid trial court may not grant any relief.