Praying and bowing down on knees and hands ( both knees and palms resting firmly on the floor with forehead also lightly touching the floor ) is how Bhutanese Buddhist pay obeisance to all Buddhas, lamas and deities.
Now days if you visit a temple you would witness devotees bowing down in this way three times towards the seat of the Lama opposite to the Kikhor / Alter/ Chhoesoum even if the seat is unoccupied. After that they will turn around towards the Kikhor ( the actual Chhoesum ) to pray and bow down three times. This practice has a devotee turning his/ her back to the Kikhor and facing the often empty seat reserved for the Lama.
When a religious prayer is being conducted, at certain point of the prayer ritual, a devotee is called upon to pray and perform this obeisance. At that time the devotee first performs the obeisance act to the Lama who is leading the prayer ritual and then turns around to perform the obeisance towards the Kikhor. It is believed that the Lama in the process of performing the prayer ritual is able to acquire the position of being the effective medium between the devotees and Buddha Spirits. Therefore. the devotees bows first to the Lama and through him to the Buddha/ Buddha Spirits. This might be something like praying to Shiva through Ganeshji for a Hindu devotee..
I still follow what I was taught at an early age. If a ritual is going on, I first bow to the Lama to pray to him for assistance to reach my prayers to the Buddha Spirits. And then face the Kikhor to offer my actual prayers and obeisance. And if I am in my home Chhoesoum or in a temple without a Lama , I simply turn to the Kikhor to offer my prayers and obeisance. I neither seek the assistance of an absent Lama nor bow down to an empty lama seat. For me the Lama and the Buddha is one and same.
In some temples that are built by a Root Lama, I suppose a devotee would probably feel the need to first pay respect to the seat that was once graced by the Lama when alive. But at the same time the image/ statue of the Root Lama would also be among the Kikhor so even directly bowing to the Kikhor should not offend the Root Lama. So I guess to each devotee his/ her own way of paying respects.
In thinking over this ritual among Buddhist, I wonder how things are done in other religion. For example, I have seen Catholics kneeling and praying to crucified form of the Christ. And Catholics also bow their head or kneel on one knee before the Priest and kiss his hand/ ring. I wonder if the devotees kneel and kiss the pulpit in the absence of the priest.