If you want the system to calculate and deduct income tax for some employees and want to manually enter the tax amount for other employees, then under Run Payroll wizard >> in Run Payroll page >> in Income Tax Computation drop down choose either ‘Compute for this month’ OR ‘Use previous month's TDS’ based on your requirement.
Then you can override the Income Tax amount for selected employees by manually entering tax amount for them in the same Run Payroll page using Override Income Tax option.
To know more, read how to override system calculated income tax?
Note: If you do not want to calculate Income Tax for all your employees then choose 'Consider Zero TDS' option under Income Tax Computation drop down