Hi Rob,

Thanks for posting in the Community!

You can untick box for SHOW IN PAY RUN in the pay rates section to not show them in your pay run. Here's how to:

1. Click on the Payroll tab.
2. Select the Payroll Settings.
3. Select Pay rates.
4. Locate Salary.
5. Untick box for Show in pay run.
6. Click on Save.

Furthermore, here's how you can enable Accrue leave on your pay category.

1. Click on the Payroll Settings.
2. Click on Pay Categories.
3. Locate Salary category.
4. Under Rate Loading tick box for Accrues leave.
5. Click on Save.

Check also this link to learn more about automatically accrue leave in QBO Payroll. 

Drop by again in the Community if you have further concerns. I'm here to help you.