I have so far only done bottom-fermented beers without transferring into a second vessel for secondary fermentation. If I wanted to do some dry hopping with this technique, when is the best time to put the hops? Towards the end of fermentation into the fermenter or into the bottles when it is bottling time?
I started dry hopping in primary as a rule. I add my dry hops after the most vigorous part of fermentation is over, about 3-4 days. Waiting a bit helps prevent more foaming I have found. However I do add the hops before the ferment is done. The reason for this is that when adding whole hops to the fermentor they are filled with a lot of air. That air can lead to some oxidation/staling. By adding the hops while there is still signs of fermentation the yeast tend to consume the oxygen limiting the oxidation of the beer some.
Yes the ferment activity does "scrub" some of the volatile aromatics out of the beer, but who cares, you just add more hops to compensate. Its a recipe issue not a process issue. Increase your normal dry hop addition by 10-15% to compensate.
I can't take credit for this technique. I heard about it on The Brewing Network from Mike McDole. I had heard about it prior to the BN, but it has been best explained there.
I suggest you do it a week or a few days before bottling. Hop aromas are volatile and the less time they are in an "open" environment the better. If you throw the hops in without a bag allow a little extra time for them to settle as well.