You may want to separate other schemata (e.g. XHTML, UBL, etc.) from your schemata.
Including version numbers in either file names or directories is a good idea.
Always separate other people's schemata that have multiple schema documents:
Use different directories.
Subdirectories are great when you want to bundle the other schemata.
Sibling directories are better when your schemata augment other existing schemata.