Hi @jwinterhobsons,
Allow me to clear things up for you regarding the way VAT codes work in QuickBooks Online (QBO).
The 20% RC SG VAT code doesn't affect any boxes when you have FRS enabled on your QBO company. If your company is eligible for FRS and you have it enabled, then the VAT code in question won't show in any of your boxes.
You can view this article for more details on which VAT codes affect which boxes when you have FRS enabled: UK Flat Rate Scheme: How does it work?
If you have other questions for me, drop them in the comments below. I'll be sure to get back to you.