First off, our school was done anywhere that was convenient at the time, still is for that matter. But, I purposefully kept math and phonics separate from our other work, in a specific space and usually done during the little girls' naptime, if possible. I dedicated a shelf in my office to both subjects and kept everything we needed there.
I purchased two large, wide Sterlite 3-drawer containers. One container housed our Abeka Place Value Cards, Arithmetic Charts, Subtraction/Addition Flashcards, Combination Dot Cards, Drill Set and any manipulatives we used on a regular basis. These manipulatives included a few rulers, play money/coins, straws...that type of thing.
On the other side, I used another Sterlite 3-drawer container, same size, to house our special sounds charts which were laminated for durability, phonics flashcards and readers.
I kept dry-erase markers, extra pencils/erasers, colored pencils, other supplies in bins on the top shelf, but for the sake of this post moved them down so you get an idea. You can also see the smaller 3-drawer container nestled between with our blend practice cards and clue word cards, which fit perfectly. We have a small dry-erase board that is partly nomadic and stored behind our shelf after use.
I'd like to say I kept all the charts neatly organized in number order, but lets be real...I usually just threw it back in the drawer and called it a day. Before a lesson, Abby would be working or playing on something while I gathered the cards for that specific lesson and then we would begin. While it wasn't the cutest setup, it was a functional solution that put everything in one place and was easy to reach from the floor which is where we did school together.