You should consider how many schema parts you have.

Maybe you'll want different directories for different namespaces.

But your directory structure should be similar to how you intend to:

• distribute you schemata

• use them in tools

• use them in applications.

Changing 'schemaLocation' attributes on 'import' and 'include' elements can be a real pain!

Changing 'schemaLocation' attributes will probably introduce bugs and so orchestrate things so you don't have to do that.