The good news is you can do it either way. But for a beginner pastel painter I would suggest doing the sky first, probably blending to achieve a smoothness, adding clouds (and even blending again if the clouds require it). Don't fill the sky all the way down to the horizon, only to those areas where you may get break through in the trees. And then to do the trees over the sky.
With blending, if you want to blend up to an edge, its useful to use a stomp or tortillion, and they can get into small areas better than a finger tip. (Or roll up a sheet of paper really, really tightly.)
If you find the pastel you laid down for the sky is interfering with the pastel you are placing for the trees, you could give the sky a light spray of fixative.

