When it comes to storing these I mostly have them in drawers.
Nothing really special about this. I keep the colored pencils and my box of drawing pastels in one drawer, misc pens/markers in another, and my permanent markers in yet another.
In my toolbox I have one divider section that is for a pencil, pen and then other sections for erasers and extra leads. (Yes, I modified my divided box so I can fit other things into it.)
I also scrapbook and so I have a large collection of markers I use for that. I do use them for minis whenever I feel the need. For these I purchased a pen binder (it may have actually been for pencils as the loops are tight on the markers.) I used to travel to crops a lot so I wanted them accessible hence the binder and not just a box, which is what I used before.
Oh and yes, in the middle that is a miniature replica of this binder done in 1:12 scale. I am working on a scrapbook dome and this will go on the table if I ever finish it.
The flap in the middle is two sided and so other pens and tools are held there.
One advantage for this binder and these type of pens which are double ended is to allow them to be stored flat. So the binder either lays flat or stands on the end so they are kept horizontal.
Some pens do better when the point (usually where the lid is) is stored down. So it depends on the pen.
Another type of pen I have is a stain pen or marker. I really think these are great for miniatures in general but especially for 1:48 scale minis. The smaller the scale the less stain we need. I can say I have a small can of stain that isn't even half gone. Partly because of using the markers, but just that the can lasts when you don't have as much staining surface. The markers really make a difference to me for application and for that reason alone they are worth the cost. There are some styles that allow one to remove the nib and refill. I haven't tried that yet, but I may one day. I keep these markers either in the top section of my toolbox or in the drawer with other stain and glue that I will show in a few days. I have three colors - only because I do a lot more painting of furniture than staining so a light medium and dark works well for my needs.
When it comes to storing pens and markers, the thing most important to me is accessibility for the project at hand. That's why I keep a variety in my toolbox divider box. It doesn't mean there aren't other ones laying about my work desk, but I try to always keep one or more in the toolbox so I could travel to a mini class/club if I ever have one to go to again.
The second thing I think important is that pens and markers don't dry out. So always recap them tightly. But if they do dry up a bit or especially a lot then I throw them out. Now those stain pens, I might try refilling. Granted some types of pens can be taken apart and parts reused for other purposes. I have done that as well.
Come back tomorrow for another organizing idea during my 31 days of organizing.
Happy Miniature Organizing!