Educational cess

it is deducted for all salaried employees whose income is taxable.

As per Section 192 the employer is required to calculate tax liability of the employees taking into account other income or benefits which the employee is likely to receive during the financial year and also after taking into accounts the the relevant deductions for which the employee would be eligible. These other information would be furnished by employee to employer. And, that tax liabilites will be deducted by employer in equal installment from monthly salary of the employee and pay it to the credit of central government.

You need to bear in mind that tax liabilities include Education Cess and also Secondry Higher Education Cess at the rate of 2% and 1% respectively. So while computing the Tax Liability of your employee you need to include Education Cess and Secondry Higher Education Cess in it. Futher, there is no seperate limit for charging Education Cess and  Secondry Higher Education Cess. Its levialbe once any person (including an individual) is liable for income tax.

Agreed with Mr IRFAN, perfect answer

Is the total educational cess 3 % is on the total tax paid or on total taxable income?

on tax payable

Yes, on all salaried employees