Better integration option when importing data split by deparements

I have a large client who has employees that work across multiple departments, there is not a clear way to use the import feature to get these to show all the pay elements in the correct departments in paycircle.

Describe the Challenge

Cannot use a large number of the reporting features, or the integration with xero as the data in paycircle is not correct. Requires a lot of manual adjustments in excel.