I haven't set up anything for VAT and don't know how to. Do I need to set up something for VAT, or does Amazon calculate it automatically during the checkout process?
1. are you VAT registered?
2. Are you a uk resident?
Same questions as above !
If you live in UK you do not need to register for VAT until your turnover is £90,000. HOWEVER, if you do not live in UK, even if your business is registered here, and you store your goods here in UK for FBA you MUST be VAT registered.
In short you need to include VAT in your sales prices, it won't be added by Amazon. So your sales price needs to be all-inclusive.
Since you're asking these questions, you need an accountant as soon as possible.
As others have said you need to consult an accountant urgently as you dont seem to have grasped the principles of VAT with asking such a basic question (sorry if that is a bit harsh).
The accountant will advise you if they think your Amazon business can be legally separated from your other business.
If it cannot be considered separately, then your prices listed on Amazon should be VAT inclusive and you will either have to account for the sales on your VAT return or subscribe to Amazon VAT Calculation Service (VCS) and send HMRC the VAT owed. Amazon will not apply VAT and will only calculate it if you so it through VCS. Amazon will apply VAT on their fees which you will be able to claim back. It would be advisable to set the Tax Code correctly on items you sell (necessary if using VCS).
If you can separate the Amazon business from your other business then there wont be any VAT to consider anyway if you are below the £90k turnover. Invoices from Amazon for fees will have VAT added but you wont be able to claim them back.