While it is true that Jesus told that converted thief on the cross "today you will be with me in paradise", we cannot really conclude that Paradise was in fact in the heart of the earth. But we can certainly conclude that it was said in anticipation of all the righteous dead being in Paradise without the shadow of a doubt (after the resurrection of Christ).My understanding of this is that, because Jesus said "today you will be with me in paradise" and since after he died He had not yet ascended to the Father, I believe that when He told the man crucified next to him that he would be with him in paradise, that he was referring to their spirits going to the same place where Abraham, Lazarus and the rest of the OT saints were, which was referred to by Abraham as a place of comfort, i.e. paradise and was also under the earth. Therefore, because Jesus said "today you will be with me in paradise" that is the only place that their spirits could have gone. In support of this, remember that Jesus on the morning of the resurrection, Jesus told Mary not to hold on to him because he had not yet ascended to the Father.
That has always been my conclusion anyway.
There are 66 references to Sheol/Hades in the OT, and not one of them connects Paradise to this abode of the dead. However, every mention of Paradise (Eden) after the Fall in the OT/NT connects it to Heaven and the New Jerusalem. Therefore it is highly unlike that Paradise itself (with the Tree of Life) was first placed in Sheol and then transferred to the New Jerusalem.