If the "Bonus exemption" is entered through IT0014 or IT0015 and generates a technical WT in the /4xx range, than you should start by looking at the current configuration.
As I mentioned before, for one employee with a "Bonus Paid" and a Bonus Exemption", do a Payroll Simulation with the "Display log" box checked, and drill down into the log to find where WTs /4xx and 80xx are created, and try to identify if both these WTs exist in the Input Table at the same point of the processing.
If you look at this screen capture of a payroll log, you wil notice that I have selected folders one by one in order to drill down into the log until I could see Functions P0014 and P0015, and a double-clic on a function or on the pcr associated with it would enable me to see the Inputs, the processing and the Output. That is most likely where WT 80xx first gets processed.
For data comming from IT2002, then you would have to search in the sub-schema for Time Processing (ZT00 in this example), which should be placed before the processing of Other Payments and Deductions (ZAP0 in this example).
As for WT /4xx, it could be created at the end of the sub-schema for processing factoring Time Data and Gross (ZAL0 in this example), at the end of the sub-schema for processing Deductions and calculating Gross (ZDDO in this example), or in the Tax Calculation sub-schema (ZTX0 in this example).