Steph...there are no "duh" moments if you don't know the answer. Only if you don't try and seek it. Treestand shooting, as you found out, is different than from flat ground. There are a few variables that change and you need to know about them.
First...the "drop". Technically, your arrow drops from the forces of gravity, which are exerted along a plane horizontal to the earth (wow...did I actually say that ?) What that means is, by shooting upward, or downward, you are shooting at an angle to the horizontal. In short terms, this means that the distance you are shooting is actually less, in terms of horizontal, than if you measure straight to the target, AND, because of that, your arrow will actually tend to fly a little higher than you expected. Don't worry why, just know that it does.
On top of that, and this one, I believe is more important for you, when shooting down, especially at a close target, we tend to just point with the bow arm and not bend at the waist. Remember, we practiced on the level and did OK, but when you shoot down and DON'T bend at the waist, your draw shortens, sometimes by several inches (that WILL make your arrows fall short) and also, your aiming, anchoring scheme is all screwed up.
When shooting from above, bend at the waist so that your bow arm and arrow arm are at the same angles to your torso as they always were in practice.......aim a bit lower on the target because of that gravity thing, and also learn where to aim on a target like this as the kill zone is a bit different in view. And always pick a small spot to hit. Wow....a mouthful !
Good shooting
Chuck