If the $ amount invoiced by the vendor differs from what we had entered on the PO, how do we account for that?  We would not know about the difference until we receive the vendor's invoice.

I know that if the amount invoiced is more, we can add it in the Additional Costs tab, but if the amount invoiced is less, we cannot enter a negative figure in the Additional Costs tab.

If we change the Unit Cost in the Invoice Tab, our clearing account will be off by the difference - to correct that would mean a journal entry.

When you enter the invoice, correct the amounts on the receipt - the system will correctly post the differences through to the clearihng, AP and IC accts. See also the thread about price differences "Price Variance on Invoice vs PO Receipt"