Hi Jay Fowl,
You're most welcome, and thanks for coming back.
Let me share with you how QuickBooks treats the two rates separately. The rate set up for your service item is use for invoicing customers or billing vendors. While the hourly/salary rates set up in the employee profile will be used for payroll.
Setting up classes for payroll allows you to maximize your capability to keep track of the job profitability by running the report mentioned above. Therefore, there's nothing to adjust after setting up the class tracking for payroll.
Drop some more questions here in the Community. We'll be glad to help.