Rune crystals can be attached to characters by a Runemaster to be able to use the spells and skills they come with. ex. clone crystal lets you use a clone attack with that character doing double damage but unbalanced next turn fire crystal lets you use fire spells prosperity helps you get more money from battles
Rune Pieces are either elemental or power-ups.
The elemental ones (water, fire, lightning, wind) can be attached to a weapon by a blacksmith to add that element to a physical attack.
The ones that are power-ups (power, skill, defense, luck) can be used to power up one character's attributes through one usage unless you use the game over glitch. hopefully that helps
The crystals contain the magical powers of the runes. Go to a rune master ( the shops with a circle on the sign post) and have them attach the crystal's power onto your characters. Then when you are in a fight, the rune command will become available for that character so he or she can use a special attack or magic spell.
The clone crystal can only be attached to characters with swords, such as Viktor. If you attach the clone crystal to him, he can perform a stronger attack, but will be weakened for one turn afterwards.
If you attach the prosperity crystal to a character, it will not give them any special powers to use in battle, but it allows you to receive extra money after defeating all enemies. There are other crystals which give you these kinds of passive abilities, such as the Fortune crystal- attach that to a character and he or she will receive extra experience points after a battle.
The wind and water rune pieces can be attached to any character's weapon by a blacksmith (the shops with a hammer on the sign post) and they have a special effect on the character's regular attack or defense. I'm not quite sure what the wind rune piece does, I think it increases defense, and the water rune piece lets the character recover a small amount of hitpoints per round. The fire and lightning rune pieces do extra damage to enemies.
Crystals are just items until you get the rune master to attach the crystal's power onto a character. A character can carry more than one crystal in their inventory, but can only have one crystal attached to his or her body. If you get the rune master to remove the rune, it will go back to being a crystal. The character must have a space in his or her inventory to carry the crystal. It can then be attached to someone else.
If you get a blacksmith to attach a rune piece to a character's weapon, it can never be removed, but you can attach more of the same type of rune piece to that weapon so that it's attribute becomes stronger.
It does take some getting used to, as this game provides poor explanations of its many different types of runes, but in all the other Suikoden games its quite clear to understand how they work.