Yes, Jesus and Mary are bodily in heaven because they are glorified for one thing. In your original post you say you are contemplating the location of heaven presumably the heaven we hope to go to someday, this is a good question. In the language of scripture, heaven is upwards, i.e, above the earth even as the created heavens are where the sun, moon, and stars are located and from where the rain falls. It is an article of the catholic faith which we recite in the creed and as it is told in scripture that Jesus ascended into heaven:
"And when he had said this, as they were looking on, he was lifted up, and a cloud took him out of their sight.
And while they were gazing into heaven as he went, behold, two men stood by them in white robes,
and said, “Men of Galilee, why do you stand looking into heaven? This Jesus, who was taken up from you into heaven, will come in the same way as you saw him go into heaven.” (Acts 1: 9-11).
St Paul says that Christ ascended far above all the heavens (Ephesians 4:10).
Heaven is also the term scripture uses as the place of God’s throne. This would be as it were the 'highest heaven, ’ the third heaven of which St Paul speaks of. “Heaven is my throne and the earth is my footstool” (Isaiah 66:1). God is seen depicted as the King and Lord of creation, enthroned above it as it were as the throne of a king on earth in his palace is placed above his subjects who are beneath it. However, also, God is everywhere and creation is in God for ‘in him we live and move and have our being.’ Scripture also speaks of God’s glory as above the heavens.
The scholastic theologians speculated about heaven of course as well as its location and what could be known about it from Holy Scripture which is the word of God. The common opinion then was that the heaven we are speaking of and to which we hope to go to someday wherein the holy angels also dwell as their natural abode is an actual corporeal place created by God, the highest created heaven which they called the empyrean heaven. This highest heaven is beyond the visible heavens, it is invisible. Although maybe this invisible heaven where the blessed souls and holy angels enjoy the beatific vision of God is in the same place as the visible heavens but which is invisible. There are quite a few references in the Holy Scriptures such as the book of Revelation and John’s visions where it says that the heavens were opened or parted; the heavens were also opened at Jesus’ baptism. Does this mean the heaven of God’s dwelling beyond the visible heavens or a vision of the heaven of God’s dwelling in the created visible heavens but which is invisible? Good question. This is something one can contemplate while reading, studying, and prayerfully meditating on scripture as well as reading what the fathers of the church, doctors and saints may have said or speculated about.
At the end of the world, God is going to create a new heavens and a new earth or renew the present one. And this is going to be heaven for us while at the same time enjoying the beatific vision.
The scriptures speak of the angels as the host of heaven or occupants of the heavens (cf. Psalm 148) and the bible begins with the words “In the beginning, God created the heavens and the earth.” It seems that the heaven the blessed souls go to after departing this life and the abode of the holy angels is some created place. This heaven is also called God’s dwelling or throne in the sense I believe that God dwells there in a special manner to the blessed. In another sense, God’s ‘natural home’ as it were is not something created as he is uncreated and not in a place as he is everywhere. Only God is everywhere which means that creatures must be somewhere, a place I think created by God. This last is a more deeply involved philosophical and theological question.
