You could set up multiple products and services within QuickBooks Online. This will allow you to set up the VAT codes correctly per item/service.
Here is a tutorial video I made in regards to fees/deductions: Matching invoices where charges have been deducted
If you need anymore help please do not hesitate to reach out to me directly.
Brilliant answer, @EmilyMockett! Thank you for that! The tutorial videos are so helpful. You should be chuffed that you have a bank of knowledge, you're a great contributor to this community.
@vickyT - I would love to know more about your business! How long have you been a sheep farmer for? Do you enjoy your job?