I did it in a slight different way.
In DirectAdmin I created different domains (lets say for now domain1.com and domain2.com).
Then when I login into FTP, I got the following structure
/domains
/domains/application
/domains/domain1
/domains/domain1/public_html
/domains/domain2
/domains/domain2/public_html
/system
Then I placed the index.php in every public_html and defined some CONSTANTS with the database connection details (host, user, pwd and port).
Also all index.php points to the same application and system directory. If I update the application or system folder, every project gets the update.
