On certain types of transactions, you have the option to split departments. There is a branch profile option that has to be enabled in order to be able to split departments on transactions.
Once the branch profile option has been enabled, you will now see a "split" button on transactions.
Once you click on the split button, you will have the option to add departments and enter the desired split percentage. There will be an error message that will be displayed if the percentage exceeds 100%.