Hello @JoBacon
You will need to also link your HMRC and QuickFile accounts. When you then go to submit a return you should then be able to select the corresponding period that HMRC are looking for, and submit it this way.
There’s more information on linking your accounts, and how to submit the returns here: HMRC Tax Accounts
Regarding the invoices, nothing changes here - it’s only the VAT return side of things at this time. You would continue to create invoices etc. as normal.
Hope this helps!