Thank you for posting here in the Community, @paul105.
Let me share some information about your payroll concern in QuickBooks Online.
You can use the Expense option to record the council business payment in the system. If you're unsure of the account to use, I suggest seeking expert advise from an accountant. They'll be able to provide additional guidance to ensure your books will be accurate.
For furloughed, you'll need to create a new pay category from the Payroll Settings. Please visit this article for the detailed instructions: COVID-19: Coronavirus Job Retention Scheme.
Also, you can check the following article for some links about the payroll tasks in QuickBooks Online: