Hi Garry,
good news! We have in our plan to add the second rate for employee (cost rate and billing rate), which will allow you to understand profit&loss also for per hour billed projects, not only for fixed price projects.
Flapps already supports different employee rates for different clients/projects. When you click the project team tab on Project details, you see the default rates that are defined for each employee. You can modify them specifically for that particular project.