וַיְדַבֵּר ה’ אֶל מֹשֶׁה בְּמִדְבַּר סִינַי בְּאֹהֶל מוֹעֵד בְּאֶחָד לַחֹדֶשׁ הַשֵּׁנִי בַּשָּׁנָה הַשֵּׁנִית לְצֵאתָם מֵאֶרֶץ מִצְרַיִם לֵאמֹר- Hashem spoke to Moshe in the Sinai Desert, in the Tent of Meeting on the first day of the second month, in the second year after the exodus from the land of Egypt, saying. (1:1)
באחד בניסן הוקם המשכן, ובאחד באייר מנאם- Rashi explains, When He came to cause His Divine Presence to rest among them, He counted them. On the first of Nissan, the Mishkan was erected, and on the first of Iyar, He counted them.
A question arises. Why weren’t they counted already by the first of Nissan?
Rashi mentions it had something to do with the shechina coming down to Bnei Yisroel and that had already occurred on the first of Nissan.
דַּבֵּר אֶל בְּנֵי יִשְׂרָאֵל וְיִקְחוּ לִי תְּרוּמָה מֵאֵת כָּל אִישׁ אֲשֶׁר יִדְּבֶנּוּ לִבּוֹ תִּקְחוּ אֶת תְּרוּמָתִי- Speak to Bnei Yisroel, and have them take for Me an offering; from every person whose heart inspires him to generosity, you shall take My offering. (Exodus 25:2)
אמרו רבותינו שלש תרומות אמורות כאן, אחת תרומת בקע לגלגלת, שנעשו מהם הא-דנים ואחת תרומת המשכן נדבת כל אחד ואחד- Rashi mentions the three times Bnei Yisroel were counted during their first year after leaving Egypt. One of them is when each member of klal Yisroel gave half a shekel for the sockets of the mishkan.
This was, of course, before the first of Nissan, before the mishkan was set up. There is a deeper meaning to the counting of Am Yisroel, as explained by the Rabbeinu Bechaya and other Rishonim. The two sets of counting are to show how we are all united; we are all one unit. (In gemara, we constantly find the connection and importance of the number 600,000.) Therefore, there was great importance to each of the two sets of counting.
The first one, which took place when Bnei Yisroel donated for the sockets of the mishkan, was to gather all the single members of Bnei Yisroel and weld them (no pun intended) into one unit. After it had already been established that we are all one unit, and the shechina had already come to rest on Am Yisroel, the time came to show how each person in klal Yisroel is an individual, even whilst they are part of the single unit; they still have their own unique way to express themselves!
The Apter Rov, the Oihev Yisroel was once asked how it is possible to love every Jew. It is written in Masechet Gittin, 6a, that the Torah has 600,000 letters to represent Bnei Yisroel. If even one letter of the Torah is missing, it is incomplete and therefore, considered pasul (unfit for use). So too, each Jew is part of a collective whole; a part that we can not exist without. Love every Jew; all of them together complete the whole unit, while still retaining their individuality and their own purpose in this world.