How do I record a non-EC bill that I need to account for reverse charge on my VAT return when on Flat Rate scheme?

Hi,

I have a major supplier that I need to is based in Macedonia (no-EC state) and after discussing with HMRC I was told that because they provide services to my company I need to account for reverse charge on my VAT return. I am evaluating ClearBooks and I was hopping by entering this as a bill with VAT treatment of "Services from Supplier Outside EU" will do that trick. But unfortunately when I generate my VAT return I do not see that this transaction has been included in the VAT return.

I was expecting that these boxes would be populated accordingly:
Box 1: with 20% of the transaction's value to account for the output tax payable on the purchase
Box 4: with 20% of the transaction's value to reclaim the input tax

Can someone please help me?

Thanks.