It is prescribed to pray in congregation when making up missed prayers, because of the report narrated by al-Bukhaari (595), Muslim (681) and al-Nasaa’i (846) from Abu Qataadah who said: We were with the Messenger of Allaah (peace and blessings of Allaah be upon him) (on a journey) and some of the people said: Why don’t you let us stop to rest (at the end of the night) O Messenger of Allaah? He said: “I am afraid that you will sleep and miss the prayer.” Bilaal said: I will keep watch for you. So they lay down and went to sleep, and Bilaal leaned back against his mount. The Messenger of Allaah (peace and blessings of Allaah be upon him) woke up and saw that the edge of the sun’s disk had risen. He said: O Bilaal, what about what you said? He said: I have never slept like that. The Messenger of Allaah (peace and blessings of Allaah be upon him) said: “Allaah took your souls when He willed and He returned them when He willed. Get up, O Bilaal, and call the people to prayer.” So Bilaal got up and called the people to prayer, and they did wudoo’, i.e., when the sun had gotten high, then he stood up and led them in prayer.
Ibn Qudaamah (may Allaah have mercy on him) said in al-Mughni (1/356): It is mustahabb to make up missed prayers in congregation. On the day of al-Khandaq, the Prophet (peace and blessings of Allaah be upon him) missed four prayers, and he made them up in congregation. And in the hadeeth of Abu Qataadah and elsewhere it says that when the Prophet made up for Fajr prayer on the day of al-Khandaq, he and his companions, he led them in offering the prayer in congregation. End quote.
Shaykh Ibn ‘Uthaymeen (may Allaah have mercy on him) said: From the hadeeth of Abu Qataadah it may also be understood that it is prescribed to offer made-up prayers in congregation if there is a group, because making up is to be done as one would have performed the prayer. If they would have offered the prayer in congregation if they had prayed on time, then when they make it up they should offer it in congregation. This is also mentioned in the Sunnah in the hadeeth of Abu Hurayrah, when the Messenger (peace and blessings of Allaah be upon him) told Bilaal to give the call to prayer, then he prayed two (Sunnah) rak’ahs of Fajr, then he led them in praying Fajr prayer in congregation. End quote from al-Sharh al-Mumti’ (2/140).
Based on this, it would have been better for you to give the call to prayer and offer the Sunnah prayers individually, then recited the iqaamah and offered the prayer in congregation, as the Prophet (peace and blessings of Allaah be upon him) did with his companions.
And Allaah knows best.