To check what is currently set up:
Click System, VAT Rates.
Select a VAT Rate and under the Record section, click VAT Return. This will show what VAT boxes on the VAT Return this VAT code will be reported on.
E.g. Vat Code 1 will have ticks as follows:
Box 1: 1st and 4th box ticked
Box 2: No ticks
Box 4: 2nd and 3rd box ticked
Box 6: 1st and 4th box ticked
Box 7: 2nd and 3rd box ticked
Box 8: No ticks
Box 9: No ticks