Andrew,
I typically cut cross sections of mackerel, and the few times I used herring, I did the same thing. About 1- 1 1/2 inches thick. Mackerel (esp. fresh mackerel) was, in my experience, a little firmer, and held together a little bit better.
Typically I just run the hook in and out along the top of the section, though the skin and catching a good portion of meat with the hook. I recently went fishing with a person in Essex who had a much more complicated method of rigging herring. He tied a loop in the end of his fishing line, threaded it through a piece of herring with a bait needle, then attached a hook to the loop, and pulled the hook back into the bait so as to hide the hook.
With the cross section routine you get a few more pieces of bait per fish.
Tight Lines.
-John L.