I've never had a successful meat/leather/bone industry. I need to figure out how to use 'autobutcher' properly, at the very least, because I discover things get very complex, very quickly.
I've found doing butchery in bursts to be the least setup-intensive way of turning animals into animal products. Butchering a large animal generates a lot of jobs all at once, and if dwarves are already nearby due to a previous batch of part-hauling jobs they'll have far less distance to travel to the new jobs.
0. Build a few butcheries, and lots and lots of tanneries, and keep them close to each other and to the food stockpile and to the location of the animals. Enable tanning on lots and lots of dwarves to match.
1. Wait until you have more animals than you have space for, and nothing much else is going on. Disable refuse hauling if necessary (see below).
2. Butcher the lot of them, leaving ~2 males and ~3 females.
3. Wait a while. What should happen is that the whole working fortress will gravitate towards the small area that all the butchering, tanning, and hauling jobs are being generated in.
As for refuse handling, I prefer to leave bones and skulls in the butchery. Cartilage, feather, and nervous tissue are removed so the [t] list isn't cluttered by unusable items, but they could stay in there too if necessary. If you'd like to move everything out of the butcher's shop anyway, do it after the rottable meat and skins have been stockpiled or tanned.
Butchery is more of a logistics challenge than anything, and DFHack doesn't really help out with that.