I am getting ready to dry hop and transfer a Double IPA to a secondary Better Bottle. If I want to take a hydrometer reading at this time is it better to use a thief or just put the hydrometer in the bucket. If I use the thief should I return the beer in the thief to the fermenter or discard it?
As brewchez says, don't return the sample wort to the fermentor - it's not worth the risk - nor the hassle. But if you really feel you want to return it, warm it to 160F first to reduce the risk of infection and wild yeast. You'll drive of a little alcohol, and maybe some aroma, but in such a small sample, it won't make much difference.
I've only ever done this once, when I accidentally pulled too large a sample before I got a wine thief. So, even though I mention it, I don't recommend it.
It's a lot easier to just brew say 10% more to allow for the samples and other losses. For a 10 gallon batch, I brew 11 gallons rather than 10, to allow for the wort samples and losses to trub in the fermentor.
Never return beer to the fermentor. Its not worth the risk of contaminating the whole batch. That is your sample to read, check for color and clarity and more importantly taste.
I think its sort of tough to read the hydrometer in the bucket, especially if you have to compete with floaties in the bucket too.
I'd use some siphon tubing and pull a sample that way. If you have a thief, then use that. I have never had one, but I imagine its convenient.