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I guess you just tick the box for 'show unique id's' and when on your club screen you'll see a series of numbers by the name. Use that for the name of your kit/logo and make a config file for it.
I ended up putting my kits in the Premier League kits folder I've got and amending the config in there because the created one I made wouldn't work for some reason.
Team weren't IN the Premier league (just picked that one at random), and I reckon it'd work with any folder and config.
Doesn't matter what folders any logo/kit/face pack are in as long as its in the "My Documents\Sports Interactive\Football Manager 2008" directory and is included in a config file. If you have trouble making your config, try fmXML and it makes the config for you, its pretty full proof as long as you have your graphics named by the correct ID#.