Allowances, by default, will be costed to the departments used on the timesheet screen, i.e., if an employee works in 3 departments, all the Allowances will be split (proportionately) across the departments used on the timesheet screen. In Other words: An employee works across 3 departments, the same amount of hours in each department. He receives a $900.00 allowance. This allowance is split equally across the three departments he worked in.
If you wish to take control of this allocation, you may nominate that the allowance be allocated to a single specific department by selecting the Cost to a Single Department checkbox and then selecting the Department from the drop-down list.
Go to Employee Details, Payments, Allowance, and Add the allowance to the employee. If the allowance has already been added, Edit the allowance.
Ensure that the:
Active box is ticked
Cost to a single department is ticked
and select the Department from the drop down list
The allowance won't be split across the three departments.