The Console client is the best option. You can set it for a service-type launch, to automatically begin when the computer starts. But if the computer is used for other intensive purposes, then the F@H program may not shut down totally. Best is to have it as a non-service launch, so you can start/stop it as needed. Get the Console program from Stanford, and simply load it into your folder. Each process would need a separate Console control. I run two instances on my P4/3.2 \setup with no conflicts. I manually control the processes from desktop icons, but the processes could also be linked in the "Start Up" portion of the main menu.
If you begin anew with the Console version, you may loose your ranking and points from all previous work. Best to query Stanford on that issue. But if you run the configuration process first, then there should be no gaps in your status and work.
F@H.. to solve mankind's maladies.. in our lifetimes!