When creating a VAT return, ‘Supplies to EC’ (box 8), which is being correctly calculated, is being added to Flat rate vat turnover (box 6), however I believe this should be excluded. As such my last VAT return I have ended up over paying as I didn’t thoroughly check the values.
The table in section 6.4 specifically says that you should include sales of goods to the EC (i.e. the things that go in box 8) in your flat rate turnover, and that this may result in you paying more VAT than you would if you weren’t on the flat rate scheme.
You don’t need to include supplies of services where the place of supply is not the UK (i.e. the recipient has to use the reverse charge in their own country), but those don’t go in box 8 anyway.
I’m afraid that documentation you linked to in the earlier (pre-edit) version of your post is at best misleading and at worst plain wrong. Firstly that section on “reverse charge” is talking about purchases, not sales, but more importantly QuickFile doesn’t actually do what the documentation there suggests. It’s long been a bugbear of mine that QuickFile uses the term “reverse charge” in many places where they are actually applying the goods dispatch/acquisition rules rather than the reverse charge (i.e. services) procedures, and I’ve asked them many many times to clear up the terminology.
When you tick “apply reverse charge” on a sales invoice in QuickFile what this actually does is to treat the sale as a dispatch of goods, zeroing out the VAT and putting the net value into box 8 on your VAT return.
What you actually need to do when you’re selling services that the recipient will need to reverse charge depends whether you’re on flat rate or normal VAT.
If you’re not on flat rate then you just zero rate the invoice. This will put the net in box 6, but nothing in box 8, which is correct (while sales like these are technically out of the scope of UK VAT VAT notice 700/12 specifically says that these kinds of supplies should go into box 6). Do not tick the “reverse charge” box as this would treat it as goods rather than services.
If you are on flat rate then (if I’m reading the document right that you linked to above) you would need to tick the “out of scope” box, because you need to exclude this sale from your box 6 flat rate turnover.
In both cases you need to put a note somewhere on the invoice (e.g. in the payment terms section) that the purchaser is responsible for accounting for their own VAT under the reverse charge procedure.
Note also that if you’re only selling services, not goods, then QuickFile can’t help you with submitting your ECSL as the software only offers the ECSL option if you have a value in box 8 (i.e. you’re selling at least some goods). You’ll have to submit your ECSL separately, and you may want to use the project tagging feature to help you gather together all your services sales to make this easier to work out.