As I know, sections are used to separate the content in diferent conceptual areas and then apply some rules (for example templates) to all the objects in a section . I your templates you can check the section of the node or the nodes that you recive in a fetch function and do some with the information. Sections are a way to organize your content in diferent areas with nodes that have to be similar.
To use diferent sites on the same installation you have to search in documentation by 'siteaccess'. Normally you have to create one siteaccess for any site you have to do. I think that is posible to specify a diferent root folder location using de config files (maybe the site.ini.append of each siteaccess).
Valenti.
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