Oh, you shouldn't do it in a crafting table.
I think one of the "default" discoveries - in the upper block - is a "magic crafting table". I forget the correct name.
Anyway, you put your wand in the correct slot, then fill out the crafting recipe as usual - crafting the blocks will drain vis from your wand.
Because this isn't a standard crafting recipe, NEI doesn't show it.
That said, you need quite a few pieces of research before the arcane stone even becomes available - but then arcane stone isn't particularly useful until later anyway.