BIGBEN: What you said and what GOOSE added to it sound ideal! Unfortunately the wind, terrain, and vegetation don't always permit setups that seem ideal, and when they don't, you have to make a seat-of-the-pants judgment about how and where to set up in relation to the wind.
If you limit yourself to always and only using one cross-wind type of setup, you'll bypass other good calling opportunities.
While you'll hear/read numerous "coyote hunting rules," the most significant one to constantly keep in mind is that when a coyote smells you, he is almost always "outta here!". I've seen early-season juveniles ignore what their nose tells them, including sticking their nose into the e-caller speaker (which would be covered with human scent), but you sure can't count on that happening regularly.
By the way, if you set your e-caller and decoy closer than 100 yards crosswind, you'll get easier, closer shots. But then, you'll have less opportunity to move and shift around for a shot.