The seven main chakras are in the yoga system. The Hindu one, to be specific. In Buddhist yoga, there are only five. The top two and bottom two of the Hindu system are combined into single chakras in the Buddhist system. Of the five in the Buddhist system, it is common to focus on only the top three.
The taoist systems (chi kung, tai chi) do not normally use the seven main yogic chakras. There are three locations where energy is stored. One is around the navel, one is around the heart, and one is in the forehead. It is best to emphasize the lowest of the three, knowing that filling it will also fill the other two.
It is possible to use both systems at the same time. Often they are described separately, though, and I think that this is what has caused the confusion. If you prefer the chakra system, as I do, it is still good to drop the excess energy into the subnavel storage area when you are done.
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Chi kung has more than one energy center and more than one storage area. You can work with all of them because that is faster than trying to reach everywhere through one particular energy center. It just happens to be important to finish up by dumping excess energy into the subnavel storage area. This prevents it from accumulating in places (like your head or heart) which cannot contain as much energy.
The chakras are all connected and parts of each other. Still, each transforms and works on a different sort of energy. If you develop each of them directly it is faster than waiting for the energy to push its way through all of the blocks in order.
It is a question of how fast you want to go.
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