The VAT exempt check box (under Settings > Accounts) allows you to choose if you want Sellery to use VAT inclusive/exclusive Amazon fees in calculating your minimum price.
If you are registered for VAT on your SellerCentral account, you can check the VAT exempt box. Sellery will no longer include VAT in your Amazon fees when calculating the minimum price.
To account for VAT on the price of your items when the VAT exempt box is checked off, you should add the VAT in the Margin field. The Pricing Overview is where you'll add that.
Please note that this is only valid for the European venues.