Typically, the higher grate will have the highest temp because heat rises. So, knowing that you may be 5 to 15 degrees higher on the top grate than the lower is usually no big deal. But, if the lower grate isn't at the temp you want, that can be more of a problem.
So, the thermometer at the lower grate is usually sufficient. If the lower grate is at cooking temp, you know the upper grate is at that temp or a little higher. If the thermometer is reading the upper grate, you can't be sure what the lower grate is because heat will seek to rise to the upper grate.
I will be building my UDS first with only 1 grate but I will put in the supports for a lower one. I have an offset smoker if I want to cook a lot more at one time, but I doubt that I will very often. In addition, I want to experiment with a diffuser.