If you have entered vendor invoices that are in a foreign currency (ie: the originating currency on the invoice is different to the functional currency being used by that Dynamics company), then you can post payments to the vendor account BUT you can't apply them at the same time.
The apply function has to happen after invoices have been posted - because the system then deals with the profit/loss on exchange calculation and posting.
So I think most users tend to do these international payments manually in Dynamics - then do their online banking after (or vice-versa)
I have seen some instances where a bank EFT file is created for international payments and submitted to the banking software.