Your process is spot on, don't change anything. Since you are billing for the time estimated, not actual, the "Budget and Billable" line type applies for your Project Planning Line. Since your actual time has no impact on the billing of the Project, the line type of "blank" is correct, since you don't want to impact either the Budget or the Billable planning lines. You invoice off the original Project Planning Lines, not the Project Ledger, so you are doing everything as you should.
The reason for the warning message is the "Apply Usage Link" on the Project. I encourage you leave that on, as it has impacts on Item Planning that you (potentially) wouldn't want to lose. If you are only doing Resource tracking (service type industry), you could potentially turn off the Apply Usage Link to avoid that message.
Finally, if you need it for planning, you could potentially suppress that message when posting Resource only lines in the Project Journal, but this would be an Extension, and only necessary if it becomes a real bother seeing the message.
P.S. Before making any changes to setup, such as the "Apply Usage Link", please test thoroughly in a Sandbox copy of your Production environment.
Best Regards,
Ben Baxter
Accent Software Inc