How are you integrating the priming sugar? If you're using a prime tab, then yeah going directly from the fermenter is fine...BUT unless yours is equipped with a spigot, trying to manitain a siphon from the fermenter and manipulating a spring fed bottling wand can be tricky.
Even with adding prime tabs to the bottles, it's easier to fill with a spigot and bottling wand, rather than a siphon and bottling wand.
If you're not using prime tabs, and are planning to use sugar, then it is best to make a sugar solution and integrate it with the beer at bottling time. Adding dry sugar to bottles is very tricky, it can lead from under carbd to over carbed beer to even bottle bombs. Also dry sugar and the co2 in the beer already can lead to gushers while filling. The sugar acts as nucleation sites, and you get what amounts to the mentos/diet coke effect, all the beer shooting out of the bottle.
So then the issue is how to do that.....Do you add it to the fermeter or secondary? How to you get it all to mix?
The problem with bottling from a primary or secondary instead of using a bottling bucket, is that since you have patiently gone and let your beer settle and clear, in order to mix the priming solution and beer effectively, you would have to stir it in the carboy which would a) kick up all that nice sediment you have patiently let fall, b) possibly oxydize the beer.
It really defeats the purpose of both a long primary/no secondary or a secondary if you have to stir up all the nice sediment you patiently waited to settle just so you can have consistent carbonation.
Why don't you just go to the hardware store and make a bottling bucket? You can find everything you need, including a spigot there.
With my bottling bucket and my dip tube, I leave no more than about 3 ounces behind, which means I can get about 52 to 54 bottles per 5 gallon batch.
Go to a hardware store and get a translucent or white bucket...but look for one where the 5 gallon mark falls way below the top of the bucket. Usually it will say 5 gallons at 3rd band from the top. (oh get the lid too....I totally regret not getting it when I did.)
Then get a spigot and make a dedicated bottling bucket. It really defeats the purpose of both a long primary/no secondary or a secondary if you have to stir up all the nice sediment you patiently waited to settle just so you can have consistent carbonation.
Mine is the translucent Leaktite brand 5 gallon container with the gallon and liter markings from Homedepot.
Here's a pic of mine from my bottling thread.
One of my dip tubes and what gets left behind.
You'll find a ton of good info here to make bottling easier.
Hope this helps you understand better.