I have been having the same problem with some of our sales, but found a video explaining what to do. This works well if you are not sending invoices to your customers, so this is really just for recording the sale receipt in QBO. I appreciate that for some, it will not be practical. 

Essentially follow these steps:

1. Create a new VAT rate called something like "VAT Margin Scheme" at 16.67% for Sales and save
2. Create a new Product/Service - Service called something like "Original Cost" - No VAT and save
3. Create a new Product/Service - Service called "Profit Made" - 16.67% VAT (tick the tax inclusive box) and save
4. Create a new Product/Service - Bundle called something like "Margin Scheme Sales Product" (you can always be more specific in the description). Select from the dropdown list "Original Cost" for the first line and the second line "Profit Made" and save.
5. When entering a relevant sales receipt, enter the Bundle name, in this case "Margin Scheme Sales Product" in Product (it will recognise what you're typing in). There will be two sections to the sale. First put the original cost in (excluding any subsequent repair/upgrade costs) and then enter in the profit. The selling price will populate automatically. Scroll down to the totals where you will see the 16.67% calculations and the VAT liability. Save

Hope this helps. I'm sure there is a video covering invoices, but we don't use them for these particular occasional sales so did not need to watch it. I'm guessing if you do use this system for invoicing, your margin will show to the customer!