The Halacha is that when one prays he should face the direction of the Holy Of Holies. R' Shmuel Horowitz writes how he would direct his prayers by way of the Holy of Holies and then up through the Chamber of Rabbainu, as it is known that Rabbainu brings all the prayers to H"Y.
It seems to me that understanding the concepts involved would evolve into a completely different modus operandi. The Holy of Holies has the aspect of above space, so one can face and direct his prayers towards the Holy of Holies, which stands in this world, but no further. Any further direction is what the RA"K calls "inner space", spiritual realms that are not confined to any space (although they might only be accessed by certain special places), and as such are present inside all of space. Thus Rabbi Nussun writes that there is no space in the universe that is bereft of the spirit of Rabbi Nachman. When praying one would face the Holy of Holies, and one would conjur the spirit of Rabbi Nachman inside of him/her praying with him, using his body to pray to H"Y.