As I have a full time job. I have set my personal allowance to zero, but based on the tax brackets in Scotland, any earning from this self employment will be subject to tax at higher tax rate. I need QB to be able to take account of this.

It's nice to see you here, craig-dundas-goo. 

You can assign transactions as personal income if you've linked your bank account to your Self-Employed account.

Then,  record your actual income through your Tax PRofile in QBSE. This will help us identify your tax bracket and will show up under the W-2 Annual Income box.

Here's how:

1. Go to the  Gear icon.
2. Select Tax Profile under Taxes. 
3. Fill in the net pay in the Your annual W2 Income box on the Tax Profile page.
4. Click Save.

You might find these articles helpful regarding the tax guide in QBSE:

• QuickBooks Self-Employed Overview
• UK Government guidelines
• Manually add transactions in QuickBooks Self-Employed
• About SA103F Categories

Keep me posted if you have other concerns or questions about QuickBooks Self-Employed. I’ll be around ready to help you. Have a great day ahead!