Dear Paul:

1. What does this notion of "God's dwelling place" mean anyway; for isn't God literally omnipresent?

Yes, God is everywhere (omnipresent), but heaven is His special dwelling place, His throne. In Isaiah 66:1-2 God says: "Thus says the Lord: The heavens are my throne, and the earth is my footstool." While God is everywhere He can reside in the Ark of Covenant that Moses built. While God is everywhere he also resides in the Eucharist and in every Tabernacle where the Eucharist is reserved throughout the world.

Heaven is a place especially created for us to be with Him. God, Himself, is outside of His creation. He is present in all of His creation, and He is present outside of His creation. Where we meet the beatific vision of God is heaven.

2. To look at it from our angle, it seems the ancients distinguished between the sky (first heaven), outer space (second heaven), and beyond the created universe (third heaven). Since Jesus apparently used the term "the heavens" to indicate where the Father is, would this mean God dwells in all three layers?

The three layers represent the created universe and the presence of God that is not necessarily part of the universe. God dwells in all of it.

3. We know now the earth to be within space like the other "heavenly" bodies. Does not God dwell here too?

God is everywhere. But God can remove Himself from a place in the sense that He removes His blessing and grace from a place.

4. Lastly, where does the notion of hell being "down" come from, and is there also any truth to this?

This is just a function of our perception or the "heavens" as up there and the Fallen Angels thrown "down". The word "fallen" implies down. Since we live in a world of gravity, when things fall, they fall downward from our orientation.

Astronauts in space have no sensation of up or down unless they have some frame of reference to imply an up or down. Their spacecraft can be upside down in reference to the earth, but they know no difference unless they orient themselves to a frame of reference.

Up and down are mere functions of our orientation living in gravity and the perspective to which we are situated. To pure spirits (God, Angels, and demons) there is no up or down since they are not material beings and have no such orientation to the material universe.

God Bless,
Bro. Ignatius Mary