You need to do what works for you ... so if this is it, then that is what you should do!!
For me ... I use the bobbin buddies where I can keep the spool and bobbin together.
I had kept them separate, but found I would sooner know that I had both, when I reached for what I needed.
I have a sewing desk, so left of me are the spools and bobbins with polyester thread.
The right drawer has the cotton spools and bobbins.
The stash of never-used-yet threads are in a multi-drawer cabinet at the other side of the room.
Like I said ... do what works for you.
We all have different circumstances, space allowances, preferences, and such.
Good that we are not all the same, isn't it?