In many Vajrayana practices we visualize our guide, the guru, above or on top of the crown of our head. This is the root guru (Tib. tseway lama,) who symbolizes and embodies all buddhas and bodhisattvas, and holds and imparts the blessings of the lineage.
Sometimes people are uncertain as to which person that should be: "When
someone receives an initiation from a master other than our own teacher, who is
supposed to be imagined in that position; the Lama on the throne, my teacher,
the lineage head? What about great teachers now deceased? What if I
am connected to two lineages?"
Before you meditate, you visualize your root guru, and considering that his lineage is also yours, then the lineage blessings come via him or her.
If you are receiving an empowerment from a member of some other lineage, at that moment, and in that tradition, he is your root guru. Receiving an initiation does not necessarily mean that you are going to do the practice later on at home, but if you are, then you will have to make some choices, which is one of the reasons not to be "promiscuous" in taking part in empowerments in too many different lineages.
When you take a highest tantric initiation such as Chakrasamvara, your root
guru will certainly be one who has given it. We will have to do as
Lord Marpa and "rank" our teachers for he said, "I have one
hundred and eight gurus, thirteen very important gurus, and I have only two most
excellent gurus – Naropa and Maitripa."
When we visualize the root guru, we see him in our mind's eye the way he actually. However at the same time, we think that he or she is the embodiment of all the others from whom you have received empowerments. As a representative of Guru Rinpoche, Buddha Shakyamuni or Vajradhara, he is also the expression of the Dharmakaya and ultimately, Emptiness.
The thing is, we need to make these choices before the practice so that we can experience the blessing that comes from confidence in the Guru and is related also, to our devotion.
The situation can get complicated: In The Life of Marpa the Translator by Trungpa Rinpoche (79):
We can only assume that the role of master and of disciple depends on what practice(s) Naropa and his teacher were doing. Sometimes one could be the guru and the other the chela, and then the roles could change.
The Refuge Tree
Each denomination, and even each lineage has a "geneological" chart that is known as the Refuge Tree. In it are represented the founders and teachers in an arrangement that symbolizes the interconnectedness of the various groups.
As the Dalai Lama explains:
Practitioners use the Refuge Tree and /or a Field of Merit to visualize their lineage and chain of devotion, of merit and of obligation and protection.
It is depicted as a wondrous tree with several branches. By means of artistic convention, even the branches at the back of the tree are indicated. In the sky overhead with the sun and the moon is usually found the samboghakaya form of the founding buddha, and the bodhisattvas and dakinis associated with the lineage. On the upper branches are the founding human members and closer to the ground, we see the 20th-century masters. Living teachers are not depicted.
At the foot of the great tree are the dharma protectors and the various kinds of offerings. At the bottom of the scroll or poster are often representations of those who are taking refuge in the particular tree. Practitioners can imagine themselves there, and also, they can imagine a forest of similar trees belonging to the other lineages knowing that the Buddha, Shakyamuni, appears above all of them.
Similar in function to a Refuge Tree is what is known as the Field of Merit.
Kamtsang Refuge Tree
Vajradhara is at the focus surrounded by the Karmapas, the Kagyu Yidams and so on. In the sky, to the right and left, are great yogis. In the lake in front of the tree are examples of the beings that live there. With the people in the foreground who are doing honour to the tree, are representatives of the various species of land animals.
When Guru Rinpoche is at the center surrounded by deities and lamas, it can be a Konchok Chi Du tree. Konchok Chi Du is the name of a cycle of tantric practices that centres on Guru Rinpoche as the embodiment of the three jewels and roots. Its origin is a complete cycle of terma of Jetsun Nyingpo's and is one of the Northern Treasures of the Nyingma.
Konchok means "Supremely Rare" and when part of the expression Konchok Sum, it means The Three Jewels (Buddha, Dharma, and Sangha; and by extension, the Three Roots: Lama, Yidam, Protector.)
lineage: The 14th Dalai Lama, in the foreword to Karmapa: The Sacred Prophecy. (New York: Kagyu Thubten Choling Publications Committee, 1999.)