There are three directories here, standard/, custom/, and contrib/.

standard/ holds the standard stylesheets. These are used no matter
what skin the user selects. If the user selects the "Classic" skin,
then *only* the standard/ stylesheets are used.

contrib/ holds "skins" that the user can select in their preferences.
skins are in directories, and they contain files with the same names
as the files in skins/standard/. Simply putting a new directory
into the contrib/ directory adds a new skin as an option in users'
preferences.

custom/ allows you to locally override the standard/ and contrib/ CSS.
If you put files into the custom/ directory with the same names as the CSS
files in skins/standard/, you can override the standard/ and contrib/
CSS. For example, if you want to override some CSS in
skins/standard/global.css, then you should create a file called "global.css"
in custom/ and put some CSS in it. The CSS you put into files in custom/ will
be used *in addition* to the CSS in skins/standard/ or the CSS in
skins/contrib/. It will apply to every skin.