There were two altars in the Beis Hamikdash. The Mizbeach Hachitzon, the outer altar used for the sacrifices, stood in the courtyard. Inside the Heichal was the Mizbeach Hapenimi, the inner altar which was used for offering Ketores.
The Alter Rebbe identifies two levels of emotional connection, two experiences of fiery love for Hashem. These two dimensions are represented by the two altars.
The outer altar represents the emotions of the conscious soul, referred to as חיצוניות הלב, the external heart. These are the feelings of love for Hashem that are developed through meditation on Hashem’s greatness.
The inner heart (פנימיות הלב), represented by the inner altar, is the essential desire which comes from the essence of the soul. This desire transcends reason and understanding. It is the implicit, powerful desire for Hashem alone that every Jew possesses.
The correlation reflects itself in the Avodah of each of the two altars.
Korban (sacrifice) comes from the word Karov, drawing close. The fire generated by meditation draws us close to Hashem. The fires of the outer altar, consume the desires of the animalistic soul. But we remain separate and the experience dissipates.
Ketores (incense) is related to the Aramaic term for a knot. A knot binds two things together so that they become one. This is the suprarational love and desire from the essence. Once revealed, this love never passes.
Tanya Igeres Hakodesh chapter 4
Likkutei Torah Sukkos, Ushavtem Mayim
Hemshech Ayin Beis chapter 212
Anticipating the destruction of the Beis Hamikdash, Shlomo Hamelech built winding passageways deep under the Temple floor. Here the Aron would be hidden so that it would never be destroyed or taken captive.
The Aron was absent from the Kodesh Hakodashim in the second Beis Hamikdash, but its presence and influence was there from deep below the surface.
Unlike the rest of the Beis Hamikdash which was completely destroyed and the other Keilim which were plundered, the Aron was untouched by the destruction.
Inside the Aron were the Luchos, with the words of the Aseres Hadibros carved into stone. Unlike written letters, where the ink and paper are ultimately separate, carved letters are one with the stone into which they are cut.
The Aron represents the essence of the Neshama. At the outer levels of our soul, we become connected to Hashem like ink on paper through the Mitzvos that we do, through our feelings and meditation. At our essential core, like the letters on the Luchos, we and Hashem are one.
The destructive forces of our animalistic soul may attack our inner Beis Hamikdash, eroding our outer levels of connection. But deep inside of us and ever present, our Yechida, our essential oneness with Hashem, is untouchable.