Mixed environment

Hello!
I hope that is the right forum.
Some brief preliminary infos: Dedicated server running CentOS 6.7.
I’ve set up three virtualhosts.
Main domain is installed in its proper directory (ex. public_html/user/mydomain) and inside this directory runs a wordpress multisite (within subfolders, no subdomain). As instruction on setting up a multisite, I’ve copied index.php and .htacces outside …/mydomain/ folder, so it is inside /user/ folder. The DNS resolves correctly.

And here we go to the problem. I’ve created another 2 vhosts subdomain : one running wordpress and the other another php script for elearning. So they reside in public_html/user/wordpress and public_html/user/elearning directories respectively and their URLs should be like: awpsite.mydomain.xx
My question is on the URLs. These two new sites are accessible only with the directory name in their URLs: so, awpsite.mydomain/wordpress or …/elearning

I know that the host resolve correctly because the .htaccess is the main root, infact if I not digit the final directory I am redirected to the main domain. Other subdomains are only accessible when pointing at their path directory, in the url.
How could I resolve this issue? I guess I need to touch .htaccess for the main domain…but

Sorry for the long post.
Regards
David