you can add paths for all newly created PHP projects from:
netbeans options > PHP section > Global include path
or you may add project specific include paths in a project's "project properties" (right click on a project in the projects view", and then choose "PHP Include Path" from the left side section.
although you are not allowed to edit a project included sources. you might as well create an additional project in Netbeans and call it like "my-include-path", then add all the folders in your desired include paths to this project. now you can edit your included files in this project.