Double Command

וְנָתַתָּ֖ אֶל־הָאָרֹ֑ן אֵ֚ת הָעֵדֻ֔ת אֲשֶׁ֥ר אֶתֵּ֖ן אֵלֶֽיךָ

וְנָתַתָּ֧ אֶת־הַכַּפֹּ֛רֶת עַל־הָאָרֹ֖ן מִלְמָ֑עְלָה וְאֶל־הָ֣אָרֹ֔ן תִּתֵּן֙ אֶת־הָ֣עֵדֻ֔ת אֲשֶׁ֥ר אֶתֵּ֖ן אֵלֶֽיךָ 

These pessukim are a mere 5 pessukim apart and the Rishonim ask why the repetition of placing the adut in the aron?  Rashi says ויש לומר: שבא ללמד שבעודו ארון לבדו בלא כפרת, יתן תחילה העדות בתוכו, ואחר כך יתן הכפרת עליו.  The repetition is teaching us that the adut is placed in the Aron before the kaporet is on.  The Ramban disagrees and holds the aron means with the kaporet so the possuk actually sounds the opposite that the adut should be placed after the kaporet is on.  Instead, he learns the possuk is explaining the function of the keruvim is as part of the place of the Shechina - נתת הכפרת עם כרוביו, שהכל דבר אחד, על הארון מלמעלה, כי אל הארון תתן את העדות אשר אתן אליך, כדי שיהיה לי כסא כבוד, כי אני אועד לך שמה (שמות ל׳:ו׳) ואשכוןב שכינתי עליהם.  In other words, according to Rashi the aron is an aron without the kaporet but according to the Ramban the aron is an aron only with the kaporet.  

According to Rashi the first pesskuim of the Aron are explaining its function as the place of the adut and then come five pessukim about the keruvim and the Torah repeats וְאֶל־הָ֣אָרֹ֔ן תִּתֵּן֙ אֶת־הָ֣עֵדֻ֔ת אֲשֶׁ֥ר אֶתֵּ֖ן אֵלֶֽיךָ to tell us that the adut has to do with the aron not with the keruvim.  The keruvim are part of the kaporet which is the place of communication between Hashem and Moshe.  These are two different parshiot.  First is the parsha of the aron and then is the parsha of the kaproet/keruvim.  In other words, we have the aron that holds the Torah, representing connection to Hashem through Torah and then the kaporet/keruvim which represents the direct connection between Hashem and Klal Yisrael.  The reason why the kaporet is on top of the aron, says the Rebbe (Likutay Sichos volume 26,) is because the connection between Klal Yisrael and Hashem represented by the keruvim is greater, is on top of the connection that exists via the Torah.  The Torah repeats the command וְאֶל־הָ֣אָרֹ֔ן תִּתֵּן֙ אֶת־הָ֣עֵדֻ֔ת אֲשֶׁ֥ר אֶתֵּ֖ן אֵלֶֽיךָ to tell us that that the kaporet/keruvim are separate from the aron.

According to the Ramban it is all one parsha about functions of the aron.  First, we are introduced to the aron as housing the Torah and then we are introduced to the kaporet/keruvim which represent the presence of the Shechina.  The Torah then repeats the command וְאֶל־הָ֣אָרֹ֔ן תִּתֵּן֙ אֶת־הָ֣עֵדֻ֔ת אֲשֶׁ֥ר אֶתֵּ֖ן אֵלֶֽיךָ to say that these two functions go hand in hand.  The presence of the Shechina is through the kaporet/keruvim only because the Torah is there.