Answer. If you experience any negative reaction to a crystal that likely means that crystal isn’t for you, either in this particular situation or it just isn’t a crystal that will generally work in harmony with your own energies. Some crystals will work better for you than others. I have no empathy with hematite for example but I’m never without a piece of selenite down my bra.
The side effects you experienced are largely psychological. And by this I mean your antipathy to that particular crystal has manifested itself in a physical way that the human body can recognise – for example pain or heat. You aren’t actually being hurt or burned, its just your mind telling you that crystal isn’t for you. And being in tune with that little inner voice is what intuitive work is all about.
In terms of what you should do with them, if you mean the ones you are having bad reactions to, try cleansing them. You could bury them in the garden for a few days to let any negative energies dissipate or you could wash them in salt (or blessed) water. Some people prefer to bathe them overnight in the light of the full moon. If you still react badly to the, after that, try buying a crystal you have a good feeling for. Any new age shop worth their salt will let you handle a few crystals to see which ones you build a rapport with.
Once you’ve found your crystal you can use it in many different ways. You can hold it during meditation, sleep with it under your pillow or simply keep it on your person. Cleanse it regularly and a good tip is to charge it on a bed of quartz. Some people prefer to charge inside a pyramid but the tip for the quartz was given to me by a lovely witch and I’ve always found it works very well. Crystals can be incorporated into ritual, possibly as a symbol for earth. They can be used with the traditional correspondences or used for the characteristics that are personal to you. To give you an example, I used goldstone in workings for new beginnings. It isn’t a commonly accepted association but its one that resonates with me. Like I said, its all about intuition and feeling your way toward what feels right. Chances are if it feels right, it is right and it will work alright.