To get the most of software systems, try this:
Record your guitar as normal. Now duplicate the track (If you plan to mix the synth with the original guitar track, or you could just work with the original file, but I don't recommend it unless you use non-destructive editing). Just before every note change, highlight a small portion of audio (usually just a few milliseconds will do, trial and error for best results), and delete the audio leaving just a bit of silence before each new note.
This will help the software better recognize the new pitch as it changes, as it will allow the software buffer to be free of stray overtones and harmonics caused by such things as fret buzz, open strings resonating, or simply moving fingers over the strings which hit random harmonics that we don't nessacarily hear, but the software attempts to read.