Each import needs two VAT entries in the books: the import VAT due and the matching deduction. The goods themselves are recorded at their cost, with customs duty, if any, as part of that cost. Freight and broker fees for bringing the goods in usually belong in the cost too, which matters when you work out the margin on each product line. Keep the import documents with the transaction, because they are your evidence for both the VAT and the duty.
Partly exempt businesses, such as those making some VAT-exempt supplies alongside taxable ones, cannot always reclaim all the VAT, so the deduction may be smaller than the VAT due. Your accountant can confirm the right proportion.