You won't be getting charged twice. That's common. Then when the IRS does send your refund they won't take the fees out again. If the IRS is taking too long to send your refund they will ask you to pay the fees, see step 3 under What happens if the IRS reduces my refund......
https://ttlc.intuit.com/community/payments/help/what-if-my-federal-refund-isn-t-enough-to-cover-my-t...
