Cost Centres/Tracking Categories can be applied individually after AutoEntry had processed the invoices also.
In the main list of invoices in the inbox, use the drop down menu to the far right to select the desired category (categories are listed by region in this example).
It can also be done when viewing a single invoice to the right hand side under the reference field.
For Line Item invoices, where a tracking category is selected in the header section, all the lines on that invoice will have that tracking category applied. Also, Just like the category and/or VAT code selection, where multiple tracking categories are in use on line items or a vat summary, the drop-down menu will display 'Multiple' in the inbox and single invoice view.