Output VAT and input VAT
The return compares the VAT you charged on sales (output VAT) with the VAT you paid on costs that you may claim (input VAT). If output is higher you pay the difference; if input is higher SARS owes you a refund.
Keep the three kinds apart
Standard-rated, zero-rated and exempt sales go in different places on the return. Mixing them up is the commonest error. Input VAT needs a valid tax invoice for every claim.
Your basis
Most vendors account on the invoice basis (VAT when the invoice is issued or paid, whichever is first). Some smaller vendors may use the payments basis. Your basis is set when you register.
How Bookkeeping & Invoicing helps
Every sale and cost carries its VAT type, VAT periods follow your category, and the figures for each tax period are worked out from your books. The deadline calendar emails you before each due date. You or your accountant submit on eFiling.
A note
This is a plain-English summary, not tax advice. Check your own case with SARS or your accountant.