How do I change the Institution page so that I can add my organisation logo etc.
The Institution page is a page shared by all users of the CourseSites environment. There is no way for you to change this and add the logo just for your institution.
What are these instructions referring to then?
Your institution can customize the Institution Page to include a custom logo and banner image. Your institution name also appears at the top of the page.
The Institution Page documentation on help.blackboard.com that you linked to is talking about functionality available to institutions (schools, organizations, etc.) who license Blackboard Learn.
CourseSites is a free platform available for instructors, so it does not provide "institutional" functionality / permissions - like the ability to customize the Institution Page. Instructors do not have the ability to customize that page, as it is a page that is seen by all users.
I hope that clarifies things for you
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