Rule # 1 is that there are no right or wrong answers... some things just seem to work better then others. I'm surprised year after year with what I see guys catch fish with. Experimentation is key and what worked one day may not work the next. As you try different things, you'll gain confidence in certain presentations and confidence is everything. Having said that, here's my preferred methods.
On my dead-stick (aka set line) I either run a small 1/8th oz jig head or a hook & split shot tipped with a live minnow. Hooked through the lips or behind the dorsal fin. In my opinion, airplane jigs and jigging raps are meant to be jigged so I use these types of bait on the rod I have in my hand.
I usually tip the treble of such baits... jigging raps, buckshot rattle spoons etc. with a whole minnow hooked through the head with one point of the treble. I don't hook through the lips because the minnow comes off too easily. I go right into the hardest part of its head. You can go in through the top of its head or up from the bottom. both work. I always start with a whole minnow and then downsize to a half or just the head if the whole minnow isn't getting bit.
I did see a guy do well before on Nipissing hooking his minnows on 2 points of a treble in a way that presented his minnow horizontal, rather then vertical.
Good luck and have fun.