Hello,
Chakras are my specialist subject, I work with a number of healing modalities that work on the subtle bodies and the energetic anatomy is one of my great loves! I'm currently finishing off a book on this subject, which has become quite some tome, and fingers crossed it will go into print!
The chakras suck energy from the world around us into the body, for the prime purpose that this vital force gives us our vitality, without it we malfunction. Each of the seven main chakras (their is a proposed eigth & various minor ones also, but they are of negligable importance for the sake of this description) draw energy into the body for various purposes ie each chakra controls certain functions. Consequently, when a chakra is out of harmony with its natural vibratory rate, the functions it controls become impaired, this can then have a trickle down effect into the meridians (the veins of the energy system) & then the physical body.
The best way to discover those chakras that are out (without having to go into the realms of clairvoyant perception, kinesiology etc) is to check your body language. You will find that you often cover those chakras that are out of synch in order to protect them, common examples are crossing the legs to protect the base chakra, crossing your arms over the sacral, solar plexus or heart chakras, holding your hand over the throat chakra when you talk, placing your forehead in your palms to cover the third eye chakra and placing a hand or hat on the top of the head to cover the crown. Incidentally people with self-worth issues often put weight on which covers the solar plexus chakra & esoterically protects it.
The chakras are so interdependent it is best not to work on one particular chakra on its own unless you are 100% sure that it is the only one out of balance, this is for the simple reason that they need to be harmonious, not under or overactive.
The simplest way is a simple meditation imaging each chakra as a flower or vortex of the appropraite colour, and working from base to crown allow each one to open, then when the crown opens, work back down closing them. It is important to close them or else you will find they start to take on negative energy, which will just succeed in damaging them again! There are other ways but they are far too complex to go into here. As for crystals, you can use quartz on any chakra, as for chakra & crystal correspondances, they differ wildly from one list to the next, there is no definitive version. You could do worse than simply pick them on basis of colour alone, for the simple reason that chakras respond particularly well to colour (and incidentally sound, which are both forms of vibrational healing working on sympathetic resonance).
Hope this helps,
Martin