i wash them furst under running water, then i usually smoke them with some white sage, to get rid of all of the negative energy, then i charge them, some under sunlight, some under moonlight (interesting fact, amethyst should never be charged under sunlight, it will loose its color).
There are different books on crystal healing that have chakra healing charts, different crystals are good for different chakras. If you have noticed, i have separated my crystals in color, red ones, orange ones and pink are for the lower chakras, green ones are for the heart and blue purple and white ones are for the top chakras. Saying that though, some of them double up and some of them are Universal and some of them are like microphones to strengthen the effect of others.. Also you have the dispersers, ones that help the energy to travel in all directions evenly..