I have submitted my last few vat returns via HMRC website not via QB. How do I record this on QB?

Hello Babrown1, 

Welcome to the Community page, 

So if you have submitted your returns through the HMRC website instead of through Quickbooks, then you just need to mark as filed in Quickbooks. 

So if you go to taxes>prepare return>click the drop-down arrow next to submit to HMRC>then mark as filed and do these steps up until the return you will need to submit next in Quickbooks.