Question: I am working on Demandware business manager where i need to change the site settings.

Going to Manage Sites> Selecting a site and going to settings,

there is a field called Cartridges where i put up a list of cartridges to be deployed for this site.

I want to add these cartridges to a different hierarchy like inside a folder.
Is there a way to define this in the Cartridges field under settings?

Answer: 
No, you cannot add cartridges into subfolders. Cartridges need to reside directly in the *version directory* on the server.
Cartridges - is a separate units (entities) and can be fully independence in workaround with full of logic and UI features. Off course, you can develop additional cartridge for your site, for example, if you need to extend your current payment systems, or you need some multi usable cartridge and you plane sell your cartridge as a, kind of plugin.

In other case, if need extend only locally feature - no needs reason to deploy new brand cartridge.

But each of cartridges you can upload to sendbox only separately. Else, if you nested 'physically' folder with different cartridge, you'll broke it all. 

Hope it will help you. Please, specify in comment your issue, if I understand this quote not quite well.