What do you prefer? And why?
 
 
edit:
What I mean is:  
automating a VSTi via assignable knobs in the synthrack or just use knobs on the GUI of the VSTi.
(using a hardware knob with MIDI learn or just use the mouse)

What?
 
Guess I don't know the difference.
 
There is synth automation that doesn't use controller data?
 
 

I'd guess he's talking about automating exposed parameters versus MIDI-Learn. Any VST effect or instrument can expose parameters that then conveniently show up in the envelope context menu and may be easily automated just like a volume envelope.
 
However, synthesizers typically have a very large number of parameters, often too many to practically list them all. Some don't expose anything except volume. For those, you need to explicitly assign a MIDI controller. It's not terribly inconvenient but does require an extra step of linking the CC to a specific knob. 
 
I always check first to see if the parameter is exposed for easy automation. So for Zebra, for example, I can automate the X/Y controllers by simply adding an envelope and choosing one of the X/Y parameters from a list. But if I want to automate an LFO's frequency, that's not one of the exposed parameters and therefore requires MIDI-Learn. Omnisphere, OTH, exposes nothing so any automation requires choosing a free CC number and assigning it to a knob.

What I mean is:  
automating a VSTi via assignable knobs in the synthrack or just use knobs on the GUI of the VSTi.
(using a hardware knob with MIDI learn or just use the mouse)
 
 
 
 

I prefer to use my MIDI controllers to control soft synths to using the knobs on the VSTi or writing in my CC or wheel data.  I can control more than one variable at a time plus I can get a more human feel to my songs as I am not in perfect time when I move the controllers.  Subtle differences in timing make a big different in how MIDI tracks sound.

Just my thoughts.

MarioD, do you often edit controller data or just record it once more? 

Roger that totally depends on how close I am to my goal.  Sometimes I will over play the vibrato on my wind controller.  If it is close to what I want I will use the find/change option to compress the range.

I mostly redo the data when using my MIDI control keyboard.  But again if I am close I will edit it.  

I have to deglitch notes when using my old guitar MIDI controller.  I do not use it for controller data as tracking is not very good on it when playing fast or on the lower strings.  I will add the controller data with my keyboard.

So as you can see there are two many variables to give a simple answer to your question.  Each track can be very different from the other tracks.

Thanks for your answer :-)