Now I'm trying to display different logos for each domain..
You'll have to write some custom code to do that.
why not for main domain as well> is it possible to for main domain also?
Mapping a domain to the main site interferes with site lookup in some instances.
Is this plugin works, folder word press installation as well, or I should install only in root dir.
You can have WP install in a folder so long ad it is configured to be the home of the website: https://codex.wordpress.org/Giving_WordPress_Its_Own_Directory