"And the Lord said unto the brother of Jared: Behold, thou shalt make a hole in the top, and also in the bottom; and when thou shalt suffer for air thou shalt unstop the hole and receive air. And if it be so that the water come in upon thee, behold, ye shall stop the hole, that ye may not perish in the flood." (Ether 2:20)

Did the Lord command the brother of Jared to make a hole at the bottom of the barge and use it as an air hole?

JOEL - Many critics have used this verse to conclude that Joseph Smith wasn't paying attention to what he was writing about. And many Book of Mormon scholars have come up with various ways to interpret exactly what was meant in this scripture.
The easiest explanation I have for it is a very simple one. There was a hole in the top of the ship and a hole in the bottom of the ship as the verse describes. During normal sailing the bottom hole would be plugged and the top one open to provide air. During the rough times at sea, when there was danger of water coming into the ship, both holes would be plugged up, as in the case described in verse 24:
"For behold, ye shall be as a whale in the midst of the sea; for the mountain waves shall dash upon you. Nevertheless, I will bring you up again out of the depths of the sea; "( Ether 2:24)
Being as "a whale in the midst of the sea", they would need to have both holes plugged up to prevent water from getting in. When they came back to the surface again, they could unstop one of the holes to get air. If the ship happened to be floating upside down when it came up they could unstop the hole in the bottom of the ship (which would now be the top) to get air.
Another possibility is that the hole at the bottom of the boat was not at the very center bottom of the ship but just above the water line. When it was time to catch some fish for food or empty the waste they simply opened the bottom hole and threw it out into the sea. Even though the seas were rough sometimes, the weight of the people and supplies, which were probably anchored in place at the bottom of the boat, would cause it to upright itself if turned over.