Yay organization! That is pretty much my battle cry, if you couldn't tell. So I want to share with all of you out there, makeup artists and plain old makeup junkies with a lot of pencils alike, one of the best items I have found thus far for keeping my kit organized, and also for just helping me find what I need quickly. The Niji Pencil Roll!
These are so incredibly useful. I bought them on Amazon for less than $10 each, and each one holds about 36 pencils. They hold regular sized pencils, as well as thicker pencils (like the NARS Velvet Matte, Velvet Golss, and Satin Lip Pencils). If you have a lot of thicker pencils like that, however, the number of pencils it will hold is going to decrease, as you have to be able to roll it up and snap it closed.
In one, I have all of my eyebrow and eyeliner pencils, and in the other I have my lip liners and lip pencils. If you have ever found yourself rummaging through a drawer or a bag looking for your black eyeliner pencil, but somehow you keep picking up the same navy pencil over and over again, despite the fact that it seems to go against the laws of physics, then I highly suggest you invest in one or two of these bad boys.