Customer estimate shows VAT included for each item, which is what I want, but when it gets converted to send pdf with email it deducts VAT by each item as totals up help?

Hello the, @markb003.

You can enable the VAT summary to see the VAT for each code used in the item.

Here's how: 

1. Select the Gear icon, then click Custom Form Styles.
2. Select the template you used for Estimate. 
3. Go to the Content tab, and click the footer section. 
4. Under Display, mark the VAT summary checkbox. 
5. Hit Done. 

Once done, delete that estimate, and recreate it using the new template.

Here's how:

1. Create an estimate.
2. Select Customise in the footer.
3. Select your custom template from the list.

I've attached an article below which you can use to personalise sales forms, like how to change the design, edit info, and reword your email message: Customise templates. 

Drop me a comment below if you have any other questions while working with QuickBooks Online. Have a great day.