Shekalim, Chapter Three, Mishnah Four
Our mishnah concludes the description of how the appropriation was made.
1) [After] he made the first appropriation, he covers [what is left] with leather covers.
a) [After he made the] second appropriation, he covers [what is left] with leather covers.
b) [But after] the third appropriation he would not cover [what was left].
c) [And why would he cover?] Lest he should forget and make a [fresh] appropriation from shekels from which had already been appropriated.
2) He would make the first appropriation on behalf of the Land of Israel, and the second on behalf of the surrounding cities, and the third on behalf of Babylon and on behalf of Medea and on behalf of [other] distant countries.
Section one: After the first appropriation, done at Pesah time, he would cover the left over shekels so that they would not be used for the next appropriation. The new shekels that were collected during the next period would be placed on top of the leather coverings. Similarly, after the second appropriation, he would cover the remaining already appropriated shekels with a leather covering and new shekels would go on top. However, after the third appropriation, done at Sukkot time, he would not cover the shekels. The mishnah then explains why he would cover after each appropriation. The reason is that we dont want shekels that have already been counted in one appropriation to count towards another appropriation. Doing so would be an ancient version of cooking the books. The leather covers were placed there to prevent this from happening. Since there is no appropriation after the third one, there was no need to cover the remaining coins.
A different explanation is offered by the Rambam. He holds that there were three large baskets in the chamber from which they would fill three smaller baskets, Aleph, Bet and Gimmel. At the first appropriation they would fill up the small basket with the Aleph on it from the first large basket and then cover the first large basket. They would then fill the small basket with the letter Bet on it from the second large basket and cover the second large basket. They would then fill the third basket from the third large basket but they would not cover that basket so that when the next appropriation time would arrive (fifteen days before Shavuot), they would know to begin filling the small basket with the Aleph from the third large basket. In this way, in the space of the year, each small basket would be filled from each larger basket.
There is yet another explanation, one which Albeck prefers. That is that the question is not and why would he cover [the first two] but rather why didnt he cover the third? The answer is that they would leave the third uncovered because the third appropriation is not really finished until the end of the year. They would leave the remaining coins uncovered to remind themselves to continue to appropriate from them and from new ones that would come in after Sukkot and not the coins underneath which had already been appropriated.
Section two: Each appropriation was symbolically attributed to different regions where Jews lived. The one performing the appropriation would at the first appropriation say, Behold this appropriation is from the Land of Israel for all of Israel and similarly for the next two. The order is the order of proximity to Jerusalem. It can be assumed that the people who live in Israel will get their shekels to the Temple first, the people who live in the bordering areas will come next and finally those living in Babylonian and Persia will bring their shekels.