ANd how do I improve my weapon using the crystals?

Kind of late but... wasn't around

Special Repair is done when the durability of your items gets to "0". This doesn't happens too much to warriors, but to my knowledge it's pretty common among mages. What happens when your item goes to "0"... all added effects are lost... that includes potency, gems, + bonus...
You will need gold and ores... (not sure if that's all)...
If the item is crappy... better buy a new one than repairing it.

Improving weapon :) :
Yellow Stone: gives + bonus (increases atk and contributes to potency)
Red Stone: Improves quality (increases atk and contributes to potency)
Violet stone: improves lvl of weapon (increases atk and contributes to potency... couldn't guess that one right :P)

Gems:
read in the website ;)... super gems add random Special effect... if you want I can post a list of the effects and prolly get images once I start playing again.

Kravenan has all the answers. we dont need to answer it again