First, my experience is limited. Most of what I'm about to say is academic, not experiential, knowledge. I've only done this once and had a nice subtle flavor, but I added to an RIS, and the roasted malts and high IBU overwhelmed the flavor of the chocolate.
I've heard of people getting just fine results by just dumping the nibs in, but you may want to consider soaking them in vodka for a couple weeks. I did 8 oz of nibs in a pint glass and soaked it for two weeks with just enough vodka to cover them all. The nibs will soak up the vodka, so you may have to add more to the glass over time. The vodka sterilizes it well enough and you can decant the cocoa butter out of suspension. The cocoa butter (I hear) will decrease head retention, so you don't want to throw that into your fermenter if you can avoid it. [*edit] Also consider slicing up a couple of vanilla beans in about 1.5 oz of vodka to give the cocoa a little bit of sweetness. The nibs are very bitter, the vanilla will open up the flavor a bit. When they're done soaking, just pour the liquid in and keep the solids out. I don't know if you'll see a significant positive effect if you add the solids, I'd imagine you can get a little bit more flavor out of them though.
I wouldn't stir them at the risk of oxygenating your beer. By the secondary, the yeast should have fermented most of the sugar, so any residual oxygen will not be used up by them and will become an off flavor. Optimally, you would put the nibs or flavoring extraction in the secondary before transfer.
If there are any more experienced brewers out there who have done this a few times, I'd like to learn more too.
