You use different colors and levels of crystals. If you look in the Library, it tells you what color (red, blue or green) crystal you need for each SA (special ability). Getting the crystals is a different story. They can be "level" with a quest on specific mobs, you can buy them or some special events give them.
Edit: If you check out the spreadsheet in my signature, I have every weapon and every SA listed (including color and level of crystal). Oh, and SA's are applied at a town blacksmith (grades C and B). I think A and S require Blacksmith of Mammon (not sure about A grade).
There's no crafting involved, the crystals are an item that you can obtain from a quest. I don't recall exactly, but the quest may start in Oren. Essentially you'll begin with a level 0 crystal that you'll have to level up to 7 through 13 (depending on the weapon you want enchanted) by killing monsters. You use the crystal on a monster before it dies and the crystal will have a chance of leveling or breaking, you also need to hunt specific monsters but the quest NPC will brief you on that.
You apply the crystal effect to an already existing weapon, so there's no crafting involved. The quest can be a pain if you're particularly unlucky, so if you have extra money laying around you'd be better off just buying the crystal. I believe you need a level 7 for a low end C weapon and a level 8 for a high end C weapon, the color of the crystal is what determines the enchantment. You can find that info in Elro's spreadsheets or various fansites.
ok so this is done completely during crafting? im not understanding the crystals part of this
in other words, I couldnt buy a flamberge and upgrade to a berserker blade and add focus to it?
*edit* sorry, I just now understood what you said in your last statement about SA's and where to apply them
thanks!
To answer your other questions, you apply an SA to an already crafted weapon. It is not a part of the crafting process. If you take a weapon to any blacksmith with it in your inventory and choose the "enhance a weapon" option he will tell you what SA's he can apply to a (non-SA'd) weapon. It will cost you a fee in Gemstones and a bit O cash, so it isn't all that cheap. For a C grade like a Homunkulus I think it was about 1.5M total. I just did a Hellknife (B grade) and it took me 222 B Gemstones (~2.7M)and 220,000 adena.
If a Weapon already has an SA on it, you will need to remove it to apply another. (The Black marketeer or blacksmith of mammon can do this.) The number of enchants (or lack) doesn't matter. You will get a SA'd weapon with the same number of enchants on it as your started with. You may not exchange or Upgrade a SA'd weapon at mammon however.
For your Flamberge, you can't go directly to Berserker. (Too many gaps between them in grade crystals.) You would be better off buying a near top C weapon from the Luxury shop and upgrading that at Mammon to top C with Ancient Adena then exchanging for the Berserker. Once you have the Berserker you can add the SA to it.
And lastly, to level a crystal to a high enough level to enchant at least a mid-C weapon your gonna need some help or a higher level char than the one who's gonna use the weapon. (Most of the time anyway.) To get at least a L7 SA Crystal you need to be able to kill mobs in Giants Cave or around Devasted Castle. Most mobs at C grade will only get you to a L5 Crystal. (Timak or Harits)