So effectively you’re issuing an invoice in AUD and receiving payment in AUD (as that’s what shows up in your bank account), but the amounts can vary depending on the exchange rates? Manager has to account for this difference somehow, and has no way of knowing that it should be allocated to foreign exchange gains / losses. Even if you could tell it that you’re happy that the invoice has been paid in full, it would need to know where the difference should go. Are you writing off the difference to encourage customer loyalty? Is it a discount for defective goods? Since Manager doesn’t see the USD aspect of the transaction, it can’t infer the foreign exchange gain / loss.
My suggestion would be to create your own clearing account and use journal entries to post to that to balance out the amounts owing on the invoices. It probably adds a few more steps than you were hoping for, but to me this seems to be an atypical workflow, and allowing users to allocate expenses to the foreign exchange gains / losses account at will for transactions in a single currency (the base currency, no less) would completely compromise the integrity and auditability of that account.