The first thing to know is where do you do the bulk of your homeschooling? At the dining room table? in the living room? the kitchen?
If you are doing the majority of your lessons in one room bookshelves make for the easiest storage if you have the space for them.
Keep what you need where you need it. For example, books for couch time go in a basket beside the couch.
Nature journals, magnifying glasses, baskets, and field guides live in a basket by the front door for foraging lessons and nature studies.
There are many different things that you may wish to keep in your homeschool binder depending on what you are required to keep and report to your school board.
There is no wrong way to organize your homeschool stuff if it is working for your family.