Did you read through the guide? http://devnet.kentico.com/docs/ecommerceguide/index.html?multisite_store_overview.htm

Hello,

We have been discussing this request via email. It is not possible to run multiple shops under single site hosted in Kentico CMS. Each shop would need to have its own site created in the CMS. I am posting the conclusion here, should anyone else need the same information:

There is currently no functionality which would allow categorizing and restricting access to orders based on parameters or user permissions. The described functionality would require reimplementation of the order editing controls with additional security permission checks and filtering. Alternatively, you could implement the order management as custom web part, which would only allow logged in user to manage orders tied to his e-shop, bypassing the need of CMS access and developing alternative CMS Desk Order management module.

Regards,
Josef Dvorak