You can file complaint case u/s.138 N.I.Act agaisnt the agent who had issued the cheque. 

Immediately contact a local advocate and serve the mandatory notice within the limitation period.

But you can not get a refund by filing the case, and you have to issue a notice under CPA and demand for a refund of such amount with interest as expeditiously as possible to save limitation period.  Contact a local advocate for filing a complaint before District Consumer Forum as getting your amount as a refund is a remedy.

You first issue a legal demand notice to him invoking section 138 NI act.

Let him give a reply  and if he is not complying with demand made, you have the options of filing criminal case against him under section 420 IPC and section 138 NI act with the police or file directly a cheque bounce case against him under section 138 NI act.

Besides you can file a money recovery suit also based on the cheque he had given.

Section 138 of NI Act and Section 420 IPC not exclusive to each other, a person can be charged with both offences simultaneously

Punjab and Haryana High Court: This petition was filed before a Single Judge Bench of Rajbir Sehrawat, J., in order to quash an FIR registered under Sections 120-B, 406, 420 of Penal Code and other subsequent proceedings arising therefrom.

Facts of the case were such that petitioner wanted to receive distributorship from “Bombay Dyeing” from alleged and was assured of the same but since the alleged refused, petitioner filed a complaint about cheating against the alleged. Petitioner was charged for conspiring under the registered FIR. It was contended by petitioner that Section 138 of Negotiable Instruments Act and Sections 420, 406 of IPC are mutually exclusive thus if the complaint has been filed under Section 138 then FIR under Sections 420 and 406 of Penal Code cannot be lodged for the same cause of action and hence liable to be quashed.

High Court stated that there is no such concept as “same cause of action” or “cause of action” in criminal jurisprudence. Once material against petitioner was found for involvement in a conspiracy then per se FIR cannot be quashed. On the contention of the offences being mutually exclusive, the court was of the view that an accused is liable to be punished from the stage of an attempt to commission of the offence and various offences like this can be charged together. It was discussed that Section 138 has a limited scope of trial and punishment for the offence and if the plea of the offences being exclusive to each other is taken then that would mean that other offences not covered under Section 138 cannot be filed. The Court found no application of Section 300 of Criminal procedure code and Article 20 of the Constitution of India. Therefore, the petition was dismissed as no ground to quash the FIR was found. [Sazid Khan v. State of Haryana,2018 SCC OnLine P&H 1733, decided on 27-07-2018]

you can register a Criminal Complaint under Section 420 of the Indian Penal Code along with a Section 138 NI Act Complaint.

There are different views taken by different High Court, however, the Hon'ble Supreme Court while differentiating the two offences had held that: 

In the prosecution under Section 138 N.I. Act, the mens rea i.e. fraudulent or dishonest intention at the time of issuance of cheque is not required to be proved. However, in the case under IPC involved herein, the issue of mens rea may be relevant. The offence punishable under Section 420 IPC is a serious one as the sentence of 7 years can be imposed. In the case under N.I. Act, there is a legal presumption that the cheque had been issued for discharging the antecedent liability and that presumption can be rebutted only by the person who draws the cheque. Such a requirement is not there in the offences under IPC. In the case under N.I. Act, if a fine is imposed, it is to be adjusted to meet the legally enforceable liability. There cannot be such a requirement in the offences under IPC. The case under N.I. Act can only be initiated by filing a complaint. However, in a case under the IPC such a condition is not necessary.

Therefore both the complaints can be filed simultaneously.