My tools ride in a tool bag.
I saw your tool bag last year and bought one just like it. So I don't have to dig through it, I just dump it out on the tailgate. When done, I just sweep the tools back into the bag. Too easy.
My big items like my come along and other stuff ride in an Eagle Creek X-Large duffle. I find that bags take up much less room than boxes and don't rattle around when driving over bumps.