What is the workflow in my case?

Say I have many sites
/var/www/site_based_on_system_1
/var/www/site_based_on_system_2
...

and all of them are based on the same system files stored in
/var/www/my_site_system

I.e. their basic functionality is extended from /var/www/mysitesystem

So when i load a project /var/www/site_based_on_system_1 in my IDE from a remote server, I get that the IDE cannot find a lot of classes (they are stored in /var/www/mysitesystem). So i create another project, and load from the remote server files from /var/www/mysitesystem. Now I go to the previous project, site_based_on_system_1, and add mysitesystem as a content root - so now the IDE can correcly detect all classes.

However when I'm in the site_based_on_system_1 project, for the main directory the autoupload works, but for the added directory it doesn't. So i have to switch to the second project and make changes from there and upload them to server. Is there a way to fix this situation?

Or maybe implement a functionaly so i could attach to one project not  just a directory, but a whole another project with it's own deployment settings