Apply prepayment Issue

We prepaid EUR22541.11 in Dec 2013 and prepaid EUR22541 in Feb 2014.We paid the two prepayments from our USD account because we have no EUR account.In May 2014 we received the invoices which in EUR,then we entry these invoices in EUR.When I apply prepayments,I find no prepayment because the prepayments were paid in USD.We cannot apply prepayment, so how can we apply prepayment these? Your advice will be appreciated. Thank you.