I think you have to be using the stock Samsung keyboard and select the settings by holding down the key next to the keyboard on the left (sorry I'm using SwiftKey at the moment). Choose handwriting to text and a handwriting keyboard will show where the keyboard normally would be and that's what will translate to text. I also don't use the stock messaging app so not sure how easy it is there.
Also, after handwriting your text you can use the selection tool and highlight your handwriting, then choose convert to and choose text. Not the best solution but it works pretty well. Maybe not for note taking.
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Yes, you have to use the Samsung Keyboard in order to do it. I use Swiftkey when I am "thumbing" it with swype. When I pull out the S-Pen, I pull down the notification bar and switch the input to Samsung keyboard, and roll on with it like you describe.
I like being able to switch on the fly depending on what I'm doing.
Most of the time, I don't use the write to text function, I just jot down my notes in S-Note or OneNote and keep on going. I will clean it up later when I pull it down to my PC for use later.
If I use the write to text function, it is so I can share the doc with team members and not have to worry about translating my chicken scratch later.