"You shall place the lid on the Aron from above, and into the Aron you shall put the Testimony that I shall give you." (Shemos 25:21) Rashi comments: "I do not know why this has been repeated, for it has already been stated, 'And you shall put into the Aron the Testimony.'" Rashi goes on to say that maybe there is meant to be specific command not to place the lid on and then remove it in order to put the luchos into it, rather the luchos must be put into the Aron before the lid is even put in place.
Last year (5771), the Rebbe explained that Rashi's self-expressed ignorance as to why the commandment of placing the luchos in the Aron is repeated offers room for one's own interpretation. He then pointed out that the implication may be that there are two aspects to Torah. One, the revealed and apparent Torah, is meant to be placed in the Aron without a lid on it, accessible simply by looking towards it and engaging in it. There is a second aspect, however, which is more delicate and illusive, more difficult to connect to. That is the Torah in the kapores, the covering itself, as referred to in the pasuk. The lid itself is a Torah that must then be placed on the Aron.