My first guess would be UNDER the bottom strand.
I've seen some cases where it was clear that the dogs were stepping between the wires, but it was easy to tell. If they're goin under, then you'll notice the game trail evenly worn under the fence. If they're going between strands, it's usually because they can't cleanly get under the wire, and there will almost always be a break in the game trail. If the game trail thins, or breaks, under the fence, then it shows that they're stepping over the wire and not treading under the fence.
Another way to tell is to check for hair in the barbs, or stuck in the wire. If the dogs are only going underneath, there's usually hair stuck in the wire or on the barbs of the low wire, but not on the upper wire. If there is hair on both lines, then they're going between. If there isn't any hair, then you can wrap on a new barb in the section where they're travelling (helps to have one to hang the snare on anyway).
In some cases, if the low wire is low, and the gap between the 2nd wire is big enough, then they can pick and choose, so the game trail will be evenly worn, and there might be hair in the bottom and top side of the lower barbs, and hair in the upper barbs as well. In that case, I string two snares, one anchored to the left, and one anchored to the right. If you anchor both to the same side, then if you catch one, it will likely knock down the second snare, and if you catch two, then the two can badly tangle/kink your snares. If you hang one to each side, you can catch two in a night without worry (handy since dogs tend to travel together).
It might also be helpful to know which direction the dogs are travelling as they cross the fence, if the game trail is too trodden to see clear prints, you can scuff down the old prints and lighten up the dirt (don't dig up too much or they'll notice). It's great for this time of year if your temps come back up above freezing, because the ground is wet, so you'll get nice clean prints.
Hope that helps a bit, it's not an exact system, but coyotes are creatures of habit.