installing modules with downloaded directories intact?

what is the best practice to installing modules?. Installing the modules with downloaded module directories intact?

i.e
-modules
- cck-5.x-1.6-1
- cck

or just placing the cck folder in the modules folder.

-modules
- cck

after placing the module folders both ways, the modules show up in Drupal's module list. But , I'm wondering if programmatically, they should be placed one way or another.