Yes if you convicted in the cheque bounce then it will effect on your job, if your really due amount to the complainant then it is better for you settle the matter before the judgement.
If you can settle this issue with to whom you issued cheque. You can also do outside court settlement. Once if you settle this issue there will be no affect on your job. If you do not settle you have to face punishment given by the court.
Section 89 of the Civil Procedure Code talks of out of court settlement through the means of Alternative Dispute Mechanism. Mediation, Conciliation, Lok Adalats are the new tools of the justice dispensing system.
In case of civil suits, out of court settlement can be brought at any stage of the suit. The only requirement to formalise the settlement is a compromise Agreement in Civil Cases.
Once the case is settled either out of court or on merits i.e, after contesting and acquitted from the case, there will be no criminal charges against you and when there are no criminal charges against you, there will not be any effect on your job. Try to settle the matter with the complainant out of court to avoid the delay of the court room proceedings.
Reference: Section 89 of the Civil Procedure Code