I don't know much about using chocolate for beer purposes but with what I've read about heating chocolate for food purposes, you should use a high quality chocolate and chop it up real small. Melt half of it in a pan, take it off the heat and put the other half in to melt on it's own at the lower temps. This is supposed to preserve the natural flavors and oils that are supposedly ruined from high heating chocolate. So, I can imagine boiling isn't a good idea.
But, I haven't worked with it in beer so take it fwiw. Either way, I'm sure your beer will be fine and tasty.