三々五々 means to go with small number members or situation that something is scattered. So your sentence is correct.

Like KIMURA-san wrote, 三々五々 means "in groups of twos and threes". However, we generally use this phrase to describe situations or what a talker sees: 授業が終わると、学生たちは、三々五々学食に集まった。 じゅぎょうがおわると　がくせいたちは　さんさんごご　がくしょくに　あつまった。 After students finished their lesson, they went to a cafeteria in groups of twos and threes. 受験者たちは、三々五々、大学に向かった。 じゅけんしゃたちは　さんさんごご　だいがくに　むかった。 Examinees headed for the university. Then, go back to your sentence. 二の三々五々で行きましょう。 Let's go in (small) groups of two. I believe that we don't use this phrase with sentences describing wills. It would sound a bit awkward. My translation would be like this: 二手に／二つのグループに分かれて行きましょう。 ふたてに／ふたつのグループに　わかれて　いきましょう。