With the help of Ninos I managed to get kind of what I wanted to 
By editing the file /etc/imscp/apache/parts/custom.conf.tpl
I achieved the following:
When a new Domain/Subdomain is created, the htaccess information is automatically created and linked via vhost definition. i-mscp automatically creates a file <domainname>.conf under the directory /etc/apache2/imscp with the above content. So I am able to manage a domain and all of the subdomains via one htpasswd and htaccess file and I don´t have to do that manually. Good thing about that, even it may not be the best solution after all, the custom.conf.tpl won´t be touched ("Any changes made to this file will be preserved on update."). so I don´t have to change that all the time.
I have to say, this is a solution specific for our development server, I would not recommend doing this on a production server!