I've done both ways, both will work. I now just let it sit for about a half hour after pulling the chiller so everything can settle near the bottom and go from there (sometimes I'll whirlpool but overall I think it's pointless as I've never noticed a difference). I plan to leave about a gallon in the kettle which contains most of the sediment. I prefer to keep it out of the carboy just because that leaves more room for beer. I've done some IPAs that contain about and inch and a half of sediment under the yeast cake in the bottom of the carboy. Even with a 6.5 gallon carboy I often don't have enough room for a full 5 gallons of finished product so I need all the real estate I can get.