I would siphon into the bottling bucket, and keep the siphon off the bottom of your fermentation bucket/carboy. You can wash that out later. Just siphon the clear beer.
This is a tough task. Not because it is difficult to control the siphon, but because we don't want to waste a single ounce of beer and the temptation always exists to lower the siphon and try to pick up the last few drops off the trub.