As difficult as it sometimes seems, speaking about God in a threefold way is essential for Christians if we are to pray truly "In the name of the Father and of the Son and of the Holy Spirit." Speaking about God in a threefold way arose historically to express the experience the early Christians had of Jesus and of the Holy Spirit.
To oversimplify, we might say that they experienced the loving God in a threefold way as beyond them, with them, and within them. They experienced God as utterly transcendent, completely beyond this world. They experienced God as present historically in Jesus. They experienced God as immanent, intimately present as Spirit within them and within their community.