Assuming you're talking about Ableton Live, with version 9 you can record the automation of your knob movements in the same track/midi/Virus channel where you got the notes.
I don't understant why you would do another midi phrase in the same channel, because you are talking about tweaking the sound, am I right?
So if this is correct you have to fight with knobs and automation only.
I usually record a midi clip with notes, then record my knobs tweaking in the same clip. Let me know if this works for you.
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