Before you can tag these expenses as EU, you need to enable the VAT reporting in FreeAgent. To do this choose Settings, VAT Registration.
Make sure 'Enable EC VAT Reporting' is checked and save your changes.
As you enter an expense, you'll now have the option to check whether it's not from the EC, or whether it relates to EC Goods, or EC Services.
If you tag an expense as EC Goods, use either 0% or Auto as your VAT setting.
FreeAgent will assume that there's acquisition tax on those goods and that box 2 needs to be filled in.
It'll work out the VAT that you would have paid on those goods if you'd bought them in the UK, depending on which category you've put the transaction into.
It'll then put that amount into box 2, and, unless you're on the flat rate scheme, it'll also put these into box 4 so that you don't pay any extra VAT on those goods.
Finally, it'll add the amount of the payment to boxes 7 and 9 of your VAT return.
Purchases of EC goods are reported the same way whether or not you're on the flat rate scheme.
If you tag an expense as EC Services, you also need to set the VAT rate as 0% so that FreeAgent doesn't reclaim input VAT.
Nothing will appear in box 2 or box 9 of your VAT return, because those boxes are just for goods.
FreeAgent will then work out the reverse charge on these services.