Organizations: Top level Course Package structure
An organization is like a Table of Contents for the course you want to publish. If you plan to publish two courses with lots of shared content, such as Introduction to Biology (for non-majors) and Introduction to Biology (for majors), they will share a large portion of the content in this course package within the Author environment. But some of it will be exclusive to the non-majors package and likewise for the majors package. The organization is where this distinction is made -- workbook pages, assessments, etc. that appear only in the majors course will be added to the majors course organization, but left out of the non-majors course organization.
A new Course Package has one organization (the default) built from a template, containing one Sequence, Unit, Module, and Page. The organization’s structure is described on the Content tab.
Think of your Course Package as the place where you create and store all the resources that you could include in a published course — the learning objectives, skills, pages, assessments, images, etc. The organizations are all the different ways you can assemble and actually publish different versions of your resources, as the "Biology for non-majors" and "Biology for majors" illustrates.