The nine boxes are the whole return, and most of the trouble with them comes from mixing up the two kinds. Boxes 1 to 5 are amounts of tax. Boxes 6 to 9 are values of supplies with the tax taken out. Once that split is clear the return stops being a form to interpret and becomes two running totals you keep as you go.
The tax boxes: 1 to 5
Box 1 is the VAT due in the period on sales and other outputs, meaning the VAT you charged. Box 2 covers VAT due on acquisitions of goods made in Northern Ireland from EU member states. Box 3 is the total VAT due, boxes 1 and 2 added together. Box 4 is the VAT reclaimed in the period on purchases and other inputs. Box 5 is the net VAT to pay to HMRC or to reclaim, the difference between box 3 and box 4, and it is the only figure that turns into money moving.
The value boxes: 6 to 9
Box 6 is the total value of sales and all other outputs excluding VAT. Box 7 is the total value of purchases and all other inputs excluding VAT. Boxes 8 and 9 cover the total value of supplies of goods, and of acquisitions of goods, with their related costs, in the Northern Ireland context. None of these is tax, and that is why a zero-rated sale belongs in box 6 despite carrying no VAT: the return reports what you sold as well as what you owe.
Calculating the return from the transactions
Take every sale, split it into net and VAT at its rate, and add the nets into box 6 and the VAT into box 1. Take every purchase you are entitled to reclaim on, split it the same way, and add the nets into box 7 and the VAT into box 4. Box 3 is box 1 plus box 2, box 5 is box 3 minus box 4. The only step that needs care is the split itself, because a VAT-inclusive figure divides rather than multiplies: at the standard rate the VAT is a sixth of the gross, not a fifth of it.
Questions people ask about vat boxes
What goes in box 1 of a VAT return?
The VAT due in the period on your sales and other outputs, meaning all the VAT you charged customers, whatever the rate.
What goes in box 4?
The VAT reclaimed in the period on purchases and other inputs: the input tax you are entitled to recover on what you bought for the business.
Does a zero-rated sale go on the return at all?
Yes. It carries no VAT so nothing reaches box 1, but its net value belongs in box 6, which reports the total value of sales excluding VAT.