I've written quite a few articles on this blog about specific gems and crystals but nothing about how to use them.  I will now correct that.  I'm just going to stick to the basics in this post.

Buying crystals and gems

It's best to buy crystals and especially gems from a reputable dealer.  It's also best, especially for a beginner, to get new ones rather than buying from a yard sale or a pawn shop.  When you but crystals from a yard sale or pawn shop there is a good chance they will have negative energy that may not be easy to remove.   Natural gems can be expensive, but lab grown ones work just as well, are less likely to have flaws, and are usually a lot less expensive.

Cleaning (or clearing) the crystal

When you get a crystal, especially a used one, it's important to clean it of negative energy or programming contrary to what you want it for.  There are several ways to do that.  One that some books recommend is to put the gem in running water for a while.  Another is to set it out in the sun for a day or two.  A third method is to just instruct the crystal to release itself of all previous programming and negative energy.  Better yet, do all three.

Once the crystal is "cleaned", you can program it according to what you want it for.

Protection

Gems and crystals can be used for protection from negative and evil influences.  If that is what you want the crystal for, than hold in your hand and instruct it to protect you.

Healing

Crystals can be an aid to healing, but are not a substitute for proper medical care.  If you want  to use a crystal for healing, instruct it by telling it to aid in healing according to God's will.  Don't tell it what specifically to heal.  Leave that up to the will of God.

Energizing

Crystals can be an aid to energizing your energy centers and bringing them into balance.  To use a crystal for energizing, ask it to share it's energy with you and put it outside in sunlight frequently to recharge.

A less common use of crystals is to help link people together.  Say, for example, that you have a child who is going off to school in another state or country or going off to fight a war.  You can use crystals to strengthen the psychic bond between you.  To do this, get two similar crystals, two small quartz crystals will work well, and hold them both in one hand, or one in each hand, and ask them to remain linked.  Then give one to the person you want to remain linked to.

Once you have programmed your crystal, you should avoid letting others handle it as that could alter the programming.

For all of these, it works best if the crystal is located where it touches the skin, but if that isn't possible, just having one is a pocket can help.  These are the basics.  You can get books on the subject if you want to get into it in more detail.  I don't have any particular favorite to recommend.