Assuming that you've downloaded a skin, you need to put it in the below:
C

Program Files\Sports Interactive\Football Manager 2007\data\skins
Then when you go into preferences in the game you'll see the "display & sound" page. At the top will be "window settings" and the name of the current skin your using. The dropdown list should show the skin you've just placed in the above folder. Select it and then make sure you've got "always reload skin on confirm" ticked. Your new skin should then display after a minute or so.
Post back if any probs...