i haven't read the manual, but i'm pretty sure there's no such option (or you misunderstood the text). you can research enchanted weapons, some armor items and trinkets in the magic tech tree and design units with those items, though. the process is the same as with the mundane weapons from the warfare tree, the only difference is that the magic items require crystal instead of metal. you can also buy those items from the shop of your cities (for hero characters), but in this case they cost gildar (gold), not crystal.

I thought it said you could in the Manual but that it required large amounts of crystals...hmm, guess I was mistaken

The manual is old, and severely in need of a revisitng--on many points. Not just that one.