in my box, I have enough room that they can lay flat in the drawer, some in the plactic trays they were bought in but my cart is another story. they're piled 3 high in some spots. i really need to order a few plier racks. I may put them in my toolbox as well because laying flat they're taking up valuable space.
I lay them all down inside two different drawers in my tool chest. No special order to any of it, they just all get put in there, some on top of one another.
I also use one of those nifty plier racks. Don't know what brand, but looks just like the one posted earlier in the thread. Really keeps them nice and organized.