Hi alect,

When you finalise the pay run in which you have recorded this advance, it will automatically create a journal to QuickBooks Online. If you haven't selected a specific account in QuickBooks Online for the pay advance category to journal to, it will be included in the default wages expenses journal to your default payment account. This is usually the Payroll Clearing account; you can double check this by going to Payroll Settings, then Chart of Accounts and clicking on Default Accounts to see what payment account you have set up. When the amount you have paid to the employee comes through your bank feed, you can then categorise the payment to this account like you would for a regular pay run. 

I am not sure what you are referring to in your second question, or specifically the 'deductions' side of it - are you deducting the amount from the employee's wages at a later date? If that's the case, the amount you pay the employee will match the amount recorded in the pay run - that is, their regular wages less this pay advance, and you would categorise this just like a regular pay run.

-Kass