There has been a basic misunderstanding of the relation of theory to practice in Buddhism, due to how it was introduced into the USA from the 1960s on, and due to cultural proclivities that lured us toward it.
If we look back on the history of Buddhism we can see that theory and practice always went together hand in hand, as we might expect from something that claims to follow the middle way. In other words nothing is to be rejected, not even thought, reasoning, conceptualization. And these are only satisfied if the mediator and the philosopher work together to define the new states of consciousness that are discovered in the meditation laboratory. And that is precisely what has happened in the history of Buddhism, the Buddha has been saying more and more interesting things throughout the ages. But of course we know that it was different schools defining each other against the others and competing for adherents. It is in this way that Buddhist Philosophy became so subtle. It started off pointing at nonduality from the illusory structure of the Indo-European worldview. But as time went on it refined this idea of nonduality a lot, so later versions of Buddhism were extremely sophisticated. The pinnacle of this development in my opinion is Hua Yen of Fa Tsang. This becomes one of the main theoretical foundations of Chan/Zen. And so when Chan/Zen was introduced it was based on this very developed form, which was said to reject all the sutras, which appealed to us, but was in fact wrong. One was not just one in one school of Buddhism but one could at the same time draw from several. For instance Zen and Pure Land seem so different but they were practiced together. And one of the sutra schools would be chosen as the theoretical background for that practice. It was not that Reason,and Theory was left out of account, but rather that these had developed to such a subtle and sophisticated level that no one saw how they could be improved. So they just became the assumed background. In Soto tradition there was more of this theorizing, than in Renzai, but still both drew their inspiration from these sutras, for instance the Platform Sutra of Hui Neng is very sophisticated even though it appears to be rustic.
Let us just think for a moment. If you don’t have a any concept of what you are doing, how are you going to do it? From a Phenomenological point of view, noesis and noema always combine meaning and sensory content. There is no such thing as stopping the mind from operating. It is as Dzong Ka Pa said, reason plays a specific role in enlightenment process. The Lankavatra suttra pushed by Bodhi Dharma which talks about Mind Only but which has the practice of stopping cognition is a Buddhist heresy because it departs from the middle way. The Buddha describes his own enlightenment journey in terms of words, and that meant it was intelligible to him, and could be expressed in words that indicated concepts.
Meditation in Hinayana entailed things like sitting around and watching corpses decompose in order to understand ones own mortality. Mahayana transformed the meaning of meditation though various more sophisticated theories that sought consistency in the doctrine of Buddhism. One of the things that assures us that we know what the Buddha really said is the inconsistency in it.
Abidharma analyzes all the sutras and attempts to work out the consistency of the Buddhas teaching at a superficial level. http://en.wikipedia.org/wiki/Abhidharma
But it was the philosophers who worked to give it deeper consistency, and to do that they had to go more deeply into the phenomena, there they discovered deeper states of consciousness, which in turn led to more sophisticated theories, and so on until we get to probably the most subtle way of looking at existence in the world, because of its refinement from the time of the Buddha right up until the present, since it was kept alive by the Tibetans, who developed a kind of Anti-zen, in which meditation is given up all together. Saying that you are to be mindful all the time is a step in that direction. In DzogChen there is no difference between Meditation and Non-Meditation, no difference between emptiness and form, no difference between the two truths.
But we have come to a turning point where we need to go beyond the fourth turning of the Wheel to a fifth turning, that is in consonance with the return of Buddhism to the other Indo-European branch which as rejected Non-Duality so vehemently. That new turning needs to take the Homeward path back to the nondual core of the Western worldview that appears when we realize that Zen/Chan and DzogChen as duals point to a deeper nondual beyond Emptiness and Void. There is no meditation at that more profound level, both Zen/Chan and DzogChen have gotten beyond that each in their own way, when they accomodated themselves to Taoism/Bon/Shintoism.