Duty and VAT help

I am being a little confused...

I have taken over from an accounts adviser and filling in the FedEx invoices on our system:

Example invoice:

Original Duty £106.35 Original VAT £358.98 Advancement Fee £12.00

I have been told to enter the Duty as £106.35 in as a total with zero VAT I have been told to enter the VAT in the VAT column as a £358.98 VAT amount I have been told to enter the Fee £12.00 in the total with zero VAT

Is this correct and do I need to do more on this. We have lots of invoices this last week or 2 and I don't want to enter them incorrectly or not report on them right.

Thanks for any help I can get