Ultimately the VAT code used, determines if that VAT journal will be presented on the VAT return, to check what VAT code was used:
Locate the journal via Nominal Enquiry
Expand it so you can see the detail line(s).
Select a particular detail line.
Click the Supplementary Information icon.
To see the VAT code used, in the bottom right, click the VAT tab. Generally VAT code 8 if used will be exempt from showing on the VAT return, any other VAT code will be presented on the VAT return.