Multiple Project Scope Issues

I have multiple projects open and added to the same window as I work on multiple things or often need to references things contained within other projects. The issue I am running into is that this method they have does not seem to be adding them as actual projects, but just adding the source folder of the other project into the current project. This is causing all sorts of issues as the scope of the project is now including those other project file directories when it should not be.  I have gone in and edited the project scope to try and exclude those other directories in the view, just to find that it won't work as they are not projects themselves, but just files added to the currently open project. 

Since they are just files added to the project, and you can't exclude them from the current scope, you end up with issues in the IDE including them in things like code completion, refactoring, Etc. Code Inspection is throwing warnings about multiple declarations when two of my projects counting items like classes with the same name/namespace. My only options was to remove the projects and only leave the original.

Am I missing something here in regards to getting PHPstorm to function properly with multiple open projects.