It would be easier for me to drill from one side. I am cutting a square hole in my drywall and drilling through a 2x4 (base for the wall frame) and then through some hardwood (don't know the exact depth). I know that the base + hardwood is at least 3" thick total. If I drill the hole from the top, then then the square hole I cut will have to be larger. I am trying to keep the hole as small as possible. BTW - I didn't want to cut a hole in the floor because it would be much harder to patch if I was to ever sell the house.
BTW - I am doing this because I want to move my sump system out to the garage. With all the pumps, it's way too noisy to be in the living room. In addition, I am adding a chiller, so that will make it even louder. Right now - I turn off the sump system when we watch TV.