In providing a solution for the difficulty of obtaining air, the Lord informed Jared: "Behold thou shall make a hole in the top thereof, and in the bottom thereof; and when thou shalt suffer for air, thou shalt unstop the hold thereof, and receive air. And if it so be that the water come in upon thee, behold, ye shall stop the hole thereof, that ye may not perish in the flood" (page 542 of the first edition).
This quotation is taken from the first edition of the Book of Mormon because the four thereofs italicized above appear in the early editions, but for some unexplainable reasons were deleted from the 1920 edition and all subsequent editions--see Ether 2:20. (Perhaps the revising committee thought they were superfluous.)
A careful reading of this verse in the first edition seems to indicate that the terms "in the top" and "in the bottom" do not refer to the barge itself. Rather, they refer to the top and bottom of something else such as a chamber or cylinder (designated here as "thereof") which could be used to admit air.
Dr. Hugh Nibley has explained the possible significance of the "thereofs" and the possibility of an air chamber as follows:
An exacting editor by removing those very significant "thereof's" has made it appear that when Jared wanted air he was to open the top window of the boat and admit fresh air from the outside. But that is not what the original edition of Book of Mormon says. For one thing, the ships had no windows communicating with the outside--"ye cannot have windows. . ." (Ether 2:23); each ship had an airtight door (Ether 2:17), and that was all. Air was received not by opening and closing doors and windows, but by unplugging air holes ("thou shalt unstop the hole thereof, and receive air. . ."), "when thou shalt suffer for air" i.e., when they were not able to open the hatches, the ships being submerged. (Ether 2:20)
This can refer only to a reserve supply of air, and indeed the brother of Jared recognizes that the people cannot possibly survive on the air contained within the ships at normal pressure: ". . .we shall perish, for in them we cannot breathe, save it is the air which is in them; therefore we shall perish." (Ether 2:19) So the Lord recommended a device for trapping (compressing) air, with a "hole in the top thereof and also in the bottom thereof," not referring to the ship but to the air chamber itself. Note the peculiar language: "unstop" does not mean to open a door or window but to unplug a vent, here called a "hole" in contrast to the door mentioned in verse 17; it is specifically an air hole--"when though shalt suffer for air, thou shalt unstop the hole thereof and receive air." (1st Ed.) When the crew find it impossible to remain on the surface--"and if it so be that the water come in upon thee" (Ether 2:20), they are to plug up the air chamber: "ye shall stop up the hole thereof, that ye may not perish in the flood." This, I believe, refers to replenishing the air supply on the surface, lest the party suffocate when submerged--"that ye may not perish in the flood." [Bookcraft, A Book of Mormon Treasury, pp. 136-137]
It is entirely feasible that such an air chamber could have been constructed in each boat. Some of the advantages of such an air chamber have been suggested by A. L. Zobell, Sr., as follows:
A tube is built from the bottom to the top of the barge, housing in both holes completely. Now we have a funnel right through the boat. Water can come into the tube as high as the water line of the vessel.
The model of the barge we have built has a stop hole both in front and in back of the tube, . . . These stop holes can easily be opened or closed as needed.
The purpose of the bottom hole is at least two-fold: First, it acted as a stabilizer to keep the barge at an even keel; second, it could be used to get rid of refuse. ("Jaredite Barges," A.L. Zobell, Sr., Improvement Era, April 1941, pp. 211, 252) [Daniel H. Ludlow, A Companion to Your Study of the Book of Mormon, pp. 313-315]