You may want to separate other schemata (e.g. XHTML, UBL, etc.) from your schemata.
Version numbers in file or directory names is a double-edged sword:
If you have version numbers, it is obvious which version you are using.
When you change versions, you may have to modify the schemaLocation pointers in your schemata.
Always separate other people's schemata that have multiple schema documents:
Use different directories so that you don't have file name collisions.
Subdirectories are great when you want to bundle the other schemata.
Sibling directories are better when your schemata augment other existing schemata.