Markers & pens were dangerous in their hands when not supervised, so they needed to be kept out of reach.
Pencils, crayons, pencil crayons, & paint brushes got left all over the place.
I used to keep them in a drawer (but the kids could reach it, so things ended up everywhere).
We tried buying several pencil cases (but they were reachable, and even if kept out of reach, things ended up everywhere, and nobody could remember which case was for which type of utensil, or where the cases were at any given time).
FINALLY, I found the Ikea "bygel" system.
I'm so happy with it! I installed ours up high, on the landing of our stairs to the basement (this way it's out of sight, I can reach & remove the cups easily, the kids can't, but it's easy for me to grab & get down for them & put it back when they need it). ALSO, everybody knows where the little cup is, all the time! No one has to wonder where that pencil case went!
I've been using this system for a while now & am thoroughly happy with it! :)
(bonus, it's pretty cheap!)