You'll need to charge a VAT-inclusive tax to your invoices and calculate tax liabilities to make payments according to the deadlines set by HMRC, Adeekue.
Since you're VAT-registered with the HMRC and your business's taxable turnover exceeds the threshold, you can add taxes at the appropriate rate on your customer transactions. As QuickBooks can automatically calculate these taxes for accurate filings, the program helps you track payment dues to avoid late returns and extra fees.
To help you set up VAT in QuickBooks Online (QBO), refer to these steps:
- Navigate to Taxes and select VAT.
- Click Set up VAT and choose the month you need to start calculating VAT from.
- Select your filing frequency and VAT accounting scheme.
- Once done, enter your 9-digit VAT registration number.
- Then, click Next and OK.

Once set up, you can track VAT from customers, assign VAT categories to products and services, check how much tax you owe, and submit returns to HMRC.
Additionally, to pay income taxes to HMRC as a self-employed individual, you must register for Self-Assessment tax using the HMRC's online services. They will calculate your tax liability based on the information you provide, and you'll need to make payments according to their deadlines.
With this, I'd also suggest consulting an accountant to assist you in managing taxes and ensuring your records are accurate.
Moreover, I'm including these references to help you manage VAT in your account:
Return to this thread if there's anything else you need assistance tracking your VAT-related transactions.