Hi there, @MikeB70.
Thank you for providing such detailed information it gives me a helpful overview of the issue.
If the full 20% VAT has recorded in the previous transaction, then, there's no need for you to enter VAT when entering on the next recording to avoid duplicate. However, if it doesn't total to 20% VAT, then, you can add VAT on the VAT column.
You may also wish to consider consulting your accountant to ensure your financial records are right.
Here's a great resource which you may find helpful: How to record Supplier prepayments for Products or Services.
For future reference, visit the articles listed on this page about managing suppliers and expenses for QBO: Manage Suppliers and Expenses for QuickBooks Online.
Please know that you can always get back to us if you have any other questions or concerns. Have a great day.