Open Sage 50 Go to Maintain Chart of accounts and create  DUE TO EMPLOYEE (Liability account)

Go to Options Tab > Defaults > Employees.  On the Employee Tab, create a deduction called DueTo Employee.    When you are creating the Employee Paycheck  put a negative amount in this field for the amount you want to hold back. 

When you have the funds for the employee, write them a vendor check debiting the Liability account and crediting the cash account.

Shirley Byard, BestBusinessStrategies.com

Based on the info you have written,  "employer decided to pay partial salary of an employee". If you take Shirley's advice you must recognize you are posting the full Salary and the taxes as if you had paid the full Salary, so the Full Salary and Taxes will be reported that way on the employee's W2 and payroll reports. Since you withheld an amount from their NET PAY,(setting up a deduction in the employee tab and entering a negative amount to reduce their net check amount)  then later you absolutely must pay the employee back the amount you deducted from their check through A/P.

Otherwise you need to set up another Salary under Pay Types in the payroll options with a proper description and the GL liability account you want. Now when you enter their paycheck, their salary will automatically calculate, on the new salary pay type you set up enter a negative amount to reduce their Gross Wages and calculate the proper taxes. Later when you want to pay them the rest of their salary,  enter the amount you want to pay them under the new Salary pay type as a positive number and let Sage calculate the proper taxes.