squelettes directory is not created by the SPIP default installation. Once created manually, it makes it possible for the webmaster to override the original files included in SPIP and any installed plugins, these mainly being the default templates for SPIP. This directory is also used to create your own special template files and to store any files that are specific to your site. The advantage of using this directory for customisation is to prevent your changes being overwritten any time that you update SPIP itself or any of the plugins that you might be using.
Just as much as you need to create this directory manually to store customised versions of files that are normally located in the squelettes directory, so must you also create sub-directories for any overriding files you create that would normally exist in sub-directories of the standard squelettes (or plugin) directory.