An excellent way to structure your class is to use Bible study on the Trinity. As for how we, as Christians, can reconcile our belief in the Trinity with the lack of proof that it exists, we must look at all the tenets of Christianity and the number of them that cannot be proven scientifically.
Bible Study: Belief in the Trinity
The definition of faith, according to Hebrews 11:1, is “being sure of what we hope for and certain of what we do not see.” By this definition, we must have faith in the existence of the Trinity because it is mentioned indirectly and because it is part of the doctrine that governs our religion. 
John 1:1-2, 14
In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning.
The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the One and Only, who came from the Father, full of grace and truth.
This passage does not reference all three parts of the Trinity but does give testimony to the divinity of Jesus and his communion with God. Before the gospels, no books in the Bible equate Jesus with God. There is the mention of the Savior who is coming, but there is no specific mention that Jesus is that Savior or that he is fully divine. In this passage, John says that Jesus existed from the beginning of time and that he was “with God,” or part of God, making him divine, before he came down to live among men.
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