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What is a root lama?
by Lama Gape

There are two types of root Lamas.  One is the Lama with whom we receive empowerments from, and enter into the practices of secret mantra with and from whom we receive oral instructions.  This is called the Root Lama of the three kindnesses.  Then there is the Lama who introduces us to the true nature of our mind.  The one with whom we truly see our own true nature is our Root Lama.  It may happen that a Lama gives us an introduction to the true nature of mind but we are not actually able to recognize it.  Then it would not be appropriate to assume that this Lama is our Root Lama.  When one recognizes the true nature of the mind this is an extemely profound realization.

In taking refuge with a lama, are you taking refuge with the lineage he is from also?:
When one takes the refuge vows with a Lama, one is taking refuge in the Buddha, the Dharma and the Sangha.  One cannot take refuge vows without a Lama.  And when one takes refuge with a Lama one is also taking refuge in the Lama in the sense that the Lama is also the sangha.  When we receive refuge vows with a Lama we receive the blessings of his lineage.  But this does not in any way limit us to the practice of a particular lineage.  All lineages take refuge in the same Buddha, Dharma and Sangha.  However if we take refuge with a Lama of a particular lineage it is likely that we have a karmic connection with that lineage.