When uploading invoices you can add a cost centre/tracking category to all invoices in that batch together. This saves time later having to apply them individually wither in AutoEntry or your accounts package.
Click on 'Add Items' as normal to upload files:
In the popup window for selecting files to be uploaded, where cost centres/tracking categories are in use for that company, click on the drop down to select the desired cost centre:
The selected code will be applied to all invoices in that upload.
After processing the selected codes can be viewed to the far right of the page in the inbox.