I don't think that JMS has overwrite files or tables in the DB as it does not create new directories when it already exists or create new MySQL tables when they already exists.

I suspect that you have created a new slave site with the same domain (url) that you deployed somewhere else and that this is this new site that you see. If you re-used the same DB with same table prefix, JMS has not overwriten it but just declared it connection parameter into the "global configuration".

To control which files are shared or copies, you have to create a JMS template rule where you specify the action = "copy" or "symbolic link" depending if you want a copy or share the files and folders.

So if you have 2 websites that have the same DB connections and the same directory on the disk, this mights be correct to display the same thing.

Verify the DB Connect present in your "global configuration" to verify the hypthesis that they are identical. Also verify the location on the disk corresponding to your website. Perhaps you point to the same place.

It configured in multisites folder. Is there is a way to rename the multisites folder. Also, Why main site in which component is installed is not integrated for single login.

It is not possible to rename the "/multisites" directory.
This is the place when JMS store its information.

Single Login or Single Sign-In is something special that require that you share the MySQL tables users, sessions and also the apache (or ISS) sessions ids.
This can NOT be decided by default because this require to share MySQL tables.
This is a configuration that you have to decide manually.
Get inspired from the tutorial video 16 that show how to share the content of extension and illustrated with the users.
In addition, apache (or IIS) are not able to share the session IDs between different domains. So special stuff is required to do that.
See our "Single Sign-In for domains" extension.
www.jms2win.com/en/joomla-multisite?page...51&category_id=1