Facepacks, kits and other graphics need to be extracted into:
My Documents\Sports Interactive\Football Manager 2011\graphics
You can organise your graphics as you see fit with folders, just be sure the associated config.xml is in the folder.
Then in game, make sure that 'Use skin cache' is unticked and 'Reload skin on confirm' is ticked in Prefrences > Display & Sound.
As for Genie scout, it is a stand alone program so you will just have to install it like any other program.