Sounds like a personal preference thing, so you'll probably get a variety of answers.
On every vertical smoker I've ever used, I like to put the probe in the hottest part of the pit, which is almost always on the top grate. Knowing how my pit runs helps. I know that my middle grate generally runs around 10* cooler than the top grate, and my bottom grate runs about another 10* cooler than the middle one. With that knowledge, I can place my meats accordingly and be pretty confident what the grate temp is at each level.
Of course, the same logic can be used to place the probe on the bottom grate, then just reverse all the numbers...this is just the way I've always done it.
Red