although the details are not very clear but what i understand is that you are asking about depositing salary of your staff into their bank accounts instead of issuing them cheques.
well, first of all you have to open the company's account in a nearby bank and then tell them that you are willing to open bank accounts for all your employees. and they will be more than happy to come to your ofc and have the forms etc filled from the employees there so there will be no need for every one to visit bank. your employees will have to give copy of cnic and copy of employment agreement to the bank staff and their account will be opened in the same branch.
at the time of payment of salary, you just have to write a letter to the bank mentioning the names of your employees and their salaries and then attach a cheque of the total amount favoring THE MANAGER BANK BRANCH CITY.
Transfer of salary in bank accounts is very easy job and saves a lot of time.