First, go to the "Main" tab, and open the budget line you'd like to allocate. Scroll to the department field, in the "General" section:

To allocate by the number of employees per department, select the "Allocate to departments per capita" option. Use the "+" button to select the departments which you'd like to include in the allocation:

To allocated by fixed percentages, use the "+" button to select the departments which you'd like to allocate to, and enter a percentage per department:

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