Although the Father, Son, and Holy Spirit are the three persons of the Godhead and although we can say of each of them that they are God, yet they work in various and distinct ways to do the work of God. The Son "proceeded forth and came from God" (John 8:42) and the Spirit "proceedeth from the Father" and is sent out by the Son (John 15:26). Yet, they all work together as one so that "these three are one" (1 John 5:7).
Now if all this seems difficult to understand, that is fine. Imagine how difficult it would be for an ant to explain to his or her ant friends the complexities of human life with only the knowledge and experience of ants. Well...it would be impossible. God is so far above us that we can only take what He has told us about Himself and take Him at His word. We may have a very elementary understanding of the concept but we are still far from any comprehensive understanding. It it just too high for us. We can say with the psalmist, "Such knowledge is too wonderful for me; it is high, I cannot attain unto it" (Psalm 139:6).
As to our prayers to God in the name of the Son (and other distinctions between the persons of the Godhead), let me comment. Generally speaking, references to God alone are references to the Father. So, to pray to God will usually refer to prayer to the Father. However, as I think I said in the article, there is nothing particularly wrong with speaking to the Son in prayer. It only changes the division of labor between the persons of the Godhead. It seems that in prayer, the Spirit intercedes to change the content of our prayer into acceptable requests (Romans 8:26-27) while the Son intercedes in our behalf at the right hand of God (Romans 8:34). What a beautiful picture God has given us!
