In the beginning was the word and the word was with God and the word was God. This is what the word "us" is referring to. It is referring to the Godhead; the Father, the Son, and the Holy Spirit. There are three personal distinctions, but they all unite to form one God.
Most of this section is taken directly from the Bible in Genesis chapters one and two. This has to do with the fact that Milton wanted to write a piece that justified the ways of God to man. There is no better way to do this than to show the reader how God is a loving, forgiving Father to us all, because even if we do not understand the Bible, it still will teach us everything we need to know. Milton also wanted to create a great Protestant work because so many Catholics had written great pieces. To do this, you have to go directly to the source; the Bible.