I used 4 oz cocoa nibs soaked in vodka as well, then added all of it to the secondary along with the beer and let it sit for a week before bottling. The chocolate aroma from the nibs is quite strong, which is what I wanted. I don't think it matters if you add the nibs to the primary or secondary. If I wasn't using a secondary, I would have just added the nibs to the primary and let it sit for a week before bottling.
I could murder a pint! -Lovejoy