I'm not sure what the confusion is, but Satan is said in the Bible to be in God's presence even now accusing all the believers for their transgressions before God. He has this "heavenly" access even after "rebelling" which is what put emnity between him and God before the Earth was created. In Revelation, (as this age comes to a conclusion) he will be permanently cast out of heaven and God's presence where he will spend eternity in the lake of fire with all the rest of creation who rejected Christ.
As far as Satan indwelling the serpent, it cannot be too hard to accept if one believes that any one of the fallen angels (demons) can possess humans and animals:
And, behold, they cried out, saying, What have we to do with thee, Jesus, thou Son of God? art thou come hither to torment us before the time? And there was a good way off from them an herd of many swine feeding. So the devils besought him, saying, If thou cast us out, suffer us to go away into the herd of swine. And he said unto them, Go. And when they were come out, they went into the herd of swine: and, behold, the whole herd of swine ran violently down a steep place into the sea, and perished in the waters. (Matthew 8:29-32)
Notice also the indication by the demons that they knew of a distant "time of torment" appointed for them. It is important when facing the question of why we must deal with these fallen angels and Satan along with all the evil they bring to this day. They have a definite appointment with judgement, just not yet.