Yup, the dropper line goes in the slot, letting the hooks hang just outside, which makes it easy to bait them before setting out the line.
And you do have to rotate the box as the hooks pay out, so that they pay out from the back side of the box. You don't want anything getting in the way of those flying hooks, or you'll have real trouble.
I like to have a heavy snap or trotline clip on the end of my trotline so that I can quickly snap the weight onto it, rather than taking time to tie it on. This is especially important when you're setting your line out in a strong current, such as along riprap.