However .. if you set your scratch disk to the top level of the drive, that is, if you have an extra dive called, say, MEDIA, and you just selct this drive as the scratch disk, FCP will do all the rest of the work in keeping track of the project elements. It will make a folder that contains all the elements of each project in it. No need for you to cahnge or remember anything.
The only time that this becomes convoluted is when you have more than one drive that you are saving to (we do this all the time), but FCP will still sort each project on each drive and as long as they are connected to the system (I prefer interanls anyway) then it will always know where everything is.
So the rule is : Don't try to help too much. Just tell FCP what drive to put stuff on.