We should not think that Buddha Shakyamuni and Padmasambhava are two totally different persons. According to the sutras, Padmasambhava is an emanation of Buddha Shakyamuni. Buddha Shakyamuni propagated the sutrayana and guided sentient beings in the form of a buddha. When propagating tantra, he manifested as Padmasambhava. Buddha Shakyamuni is the teacher of all the practitioners of the Theravada, Mahayana and Vajrayana. No other buddha or bodhisattva can exceed the qualities of Buddha Shakyamuni. However, due to the different aspirations of each buddha and bodhisattva, they manifest different emanations and function differently.
[Excerpt from Luminous Wisdom Book Series ~ The Guru Yoga Practice of the Seven-Line Prayer to Padmasambhava]