If your employee works at a rate other than 100% within the company, there are different things to consider.
Employee's parameters :
Your employee must be registered with the correct occupation rate which is defined in Employee > Employment:
Enter your employee's monthly wage under "Payroll data".
It is important to note that 21.AbaSalary will automatically apply a pro-rata calculation in order to adjust the wage to the occupation rate. You therefore need to enter your employee's monthly wage as if they were working at 100%.
Once you have entered your employee's monthly wage and all the other parameters, you can start counting. Here is the calculation done by 21.AbaSalary :
Wage entered in the payroll data * employment rate / 100 = salary paid
In the example below: 12'500 * 50 / 100 = 6'250 CHF