Well, you need to be sure =)
GPU folding is different than just regular cpu folding in that you need to go get a different client and you cannot run them from the same folder (maybe diff sub folders is ok, but you need to look closely and make sure they do not share any of the same files or subfolders themselves.)
Maybe you should make a c:\program files\F@H\ then make a CPU folder and a GPU folder and put the files for the respective clients into their correct folders.
Also, if you are running the FAH cpu client as a service, just let it go. No need to click anything to start it. You can see if it is running by checking task manager.
(to start or stop it, go into administrative programs, services and look for FAH, right click to start or stop)