How do I account for the invoices of a company who secured a tax refund for us, paying us the balance having deducted their fees. ?

You need to enter a receipt and a payment equal to their fee e.g. your tax refund should have been £1,000 but you only received £500 because their fee was £500. The bank receipt of £500 would be allocated to the tax refund you then create a payment of £500 to the supplier and enter another receipt of £500 to your tax refund. This supplier payment and second receipt contra each other on your bank account.