Modules and Root Module Folder Usage

Imported From: http://groups.google.com/group/in-portal-dev/browse_thread/thread/72ffd18c2afa26d5#

We need to setup a root folder for each module, and all folders have module's tab to hold all types of content. For example, we can create news in root folder of In-News, but also in another folder at the same level (ie. not a subfolder of in-news root folder), and create also news in here.

What will be the main differences between content managed under root folder, and content in other folders? I've noticed for example that news total counts all news in all folders. Is there something else we should know to avoid any error in structure setup?