Are you talking about going from primary to secondary or from the boiling kettle to the primary?
The answer is different depending on exactly what you are doing.
You can do it either way. Just make sure that the wort is cooled down. Don't want to shatter the carboy! If you use a funnel it will also areate your wort, so you won't have to shake around the carboy as much. The only time I siphon the wort is when I am trying to keep alot of trub out of the primary...usually if I am making a lighter beer.
From kettle to primary you want to oxygenate so, yeah, the funnel method is probably better. Either is really fine though.
I haven't made a decision on the trub. Some claim that the finished product is more clear and they may be right. I haven't noticed a difference but I haven't really experimented with isolating the trub that much. Once actually.
I've been pouring the whole pot in my primary for years and it works just fine. Straining is a pain in the ass. Everything that goes into the primary will eventually fall to the bottom in a tidy compact cake so why worry about it?