I have tried to ask this question a few days ago but I'm afraid it was not clear enough, so here's another try.

I have set up a LAMP-server using ISPConfig 3 for the administration. PHP is running over Fast-CGI.

I have several domains, like my_site.com, my_site.net and my_site.org, but they all point to the same application/website. Each domain has its own web-root-folder and is running under its own user. The application itself is in a common directory which is owned by another user, like so:

# path to my_application (owned by web1)
/var/www/clients/client1/web1/web/my_application/

# sym-link to my_application from my_site.com-web-root (owned by web5) 
/var/www/my_site.com/web -> /var/www/clients/client1/web1/web/ 

# sym-link to my_application from my_site.net (owned by web4) 
/var/www/my_site.net/web -> /var/www/clients/client1/web1/web/ 

With a setup like this I have encountered a few problems concerning the permissions when performing filesystem-operations with PHP. For instance, if the application is called via my_site.com, the user web5 is trying to write something to the application-folder. But the application-folder is owned by the user web1, so web5 is not allowed to write there.

As far as I unterstand, this is how Fast-CGI works.

After some research and asking a few people, the solution seems to be to break it all down to one domain (e.g. my_site.com) and define the other domains (my_site.org, my_site.net) as alias for this one domain. That way, there would be only one user who has all necessary permissions.

However, this would mean that we'd have to buy a multidomain SSL-certificate - but we already have an SSL-certificate for each domain. We were able to use them with our previous provider (managed hosting), and there we also had only one web-directory and multiple domains.

So if this was possible, I wonder: Is putting all the domains together into one v-host with one main- and several alias-domains the right approach in this case? Or may I have misunderstood something?