Hi. What is the best way to add and categorise the HMRC payment that covers the CJRS?

You can add the HMRC payment that covers the CJRS as a Bank Deposit transaction, then categorise it under an income account, matt-hayes. This way, you'll be able to record the HMRC payment in your QuickBooks Online account.

The HMRC payment with the CJRS is considered an income to your account. It's the amount that's given by the agency for your employee's  furlough due to Coronavirus (COVID-19). If you're able to locate the payment in your account's downloaded transactions, then you can categorize and add it to QuickBooks.

If the payment transaction isn't in your downloaded transactions, you'll have to record it manually as a Bank Deposit. Let me guide you how.

1. Go to the +New button.
2. Select Bank Deposit.
3. From the Account drop-down, choose the income account you wan to deposit the payment.
4. Enter all the needed details.
5. Select Save and close.

I've attached screenshots below for your reference.

Moreover, in case you're using the Advanced Payroll version for QBO UK, you can check out this link to effectively manage your payroll and employees: QuickBooks Online Advanced Payroll. It also contains articles about leave and statutory payments, expense and timesheets, and reports and pensions.

In addition, I've also added an article about the Coronavirus Job Retention Scheme (CJRS) to learn more about it: CJRS: What you need to do.

Please let me know if you have other concerns. I'm just around to help.