When using reverse charge vat code (RC SG) on suppliers invoices for the new CIS reverse charge , it adds the value of the sale to Box 6 on vat return? But it shouln't?

I'll help with your question about VAT codes in QuickBooks Online, alison.harding.

The RC SG VAT code adds either a positive or a negative value to Box 6 and 7 when used in an expense transaction.

With regards to your  second questions, the RC SG codes can only be used for purchase transactions. It is not applicable for sales transactions such as invoices and sales receipt. Let me share this article for more details: Common VAT Codes. 

I would also recommend reaching out to your accountant to check what code to use for your invoices so not VAT is charged. 

More details about tracking VAT are discussed here:

• VAT Getting Started
• Set Up And Edit VAT Settings, VAT Codes, And VAT Rates

Don't hesitate to reply below if you still need more help when tracking your VAT in QuickBooks Online.