The mentioned book is pretty awesome. That's what I've been using for ages. Also, perform the ritual for Abrasax, and kindly ask Him to guide you and teach you about these things.
I have tried a few different methods for the use of crystals.
Before anything, it's important to first cleanse it. Personally, I use Demonic blue energy for this purpose. Alternatively, you can place the stone out in the Sun and program the energy of the Sun to cleanse it. Some texts mention cleansing with water, but this is not meant to be taken literally - it refers to the purifying properties of the element of water. Although I would suppose that submerging the stone in water and impregnating it with the water element and programming it to purify the stone would also be effective.
I have experimented with simply carrying the stones (just for the sake of experimentation) without any purification or charging, but as expected, I did not do anything.
I have performed one-shot workings where I would purify a stone and imbue it with the corresponding rune. I would vibrate the rune into the stone around 50 times and then carry it with me at all times. While this method has been effective, the effects tend to dissipate rather quickly.
Additionally, this method can also be used to imbue stones with specific energies that can influence individuals. For instance, my ex-girlfriend had too much masculine energy and we tried to fix that, I charged a moonstone with the energy of the actual Moon and the rune Berkano (and another two that I can't remember at the moment). She carried the stone and it actually worked to amplify her feminine energies. However, the effects also wore off after a week or two, so the stone needed to be recharged.
One of the most powerful and long-lasting methods of working with stones is to perform a 40-day working while carrying the stone with you at all times. During the working/meditation, you can visualize the stone amplifying or absorbing the desired energies. In addition to the tips on the Runes page, you can also consult the astrology section to determine which stone would be best suited for a particular type of energy. For instance, I have used black onyx stones extensively in Saturn-related workings.
I have also used the stones with the squares in a similar fashion.
One cool thing you can do is go find them in Nature. Try to find a list of the areas where you can find specific kinds of stones.