Balance in: Writing on a score vs just reading.

I would say the best system is repetition and being creative. Try your ideas and see what you like and see how you can apply that creativity to your learning. Have fun:)

If the harmonies aren’t yet jumping out at you, I’d highly recommend writing them in. If you don’t wish to mark up printed editions too much, you can always make a paper or digital copy. Digital sheet music has the advantage of offering layers, so you can create a layer just for the harmonic analysis and switch it off if you no longer need it.

With practice, you’ll eventually get to the point where you’ll recognize the common harmonies such as all the triads and most seventh chords more or less at a glance. Best of luck!

Hello.  I almost always do harmonic analysis right on my score as I am learning a piece.  If I want to do a lot of markup, I will make a photocopy and do the analysis there.   Sometimes I even use coloured pencils to highlight certain progressions, or structure, etc.  I do this mainly because it enriches my relationship with the piece!  But it helps me learn it too.  And over time, it helps with sight reading and develops my ear.  

Hi Michael. After reading you, I looked at tonebase home page for Theory courses with Ben Laude. There are 3 different courses. I recommend you start looking at these as you are already in tonebase. Of the 3 courses I've only watched 1 (Basic theory, it's very good!)

I don’t like to muck up my good scores with all that. I make copies for study, or use a cheap publication like Kalmus, or schirmer

If you are wanting concise analysis annotations in the music that you are using to learn and play, you may prefer "root / quality chord symbols" (ie. G, Cm, D7/A etc.). Essentially, they are equivalent of the chords over the top of a lead sheet or what some people call the "guitar chords" in a guitar / vocals / piano format. The other common approach is 'functional chord symbols" (often also called roman numeral analysis). Roman numerals are good for conveying what is going on horizontally within the key, with the various layers (voices) forming chords that move toward cadence points. Root / quality symbols give much of the same information but are more useful for having an immediate reference to what is literally going on vertically in any particular moment (though they d not explain how these chords are interacting with each other in the key).  A command of both systems is very important for late intermediate studies and beyond but you can elect to use them as you see fit in your score for better understanding the music you are playing.

In my experience, my students tend to favor using root / quality chord symbols in their music for quick reminders. For instance, rather than marking a chord's function as V4/3 in C Major , they will simply write G7/D. This acts as a quick reminder and they can glance at the notes on the staff to remind themselves of the particular way it is voiced. 

As another person suggested, you can try things and see what works best for you. There is nothing wrong with combining elements of functional symbols and chord / quality symbols (or other systems) when it is for your own understanding. In general though, the more streamlined you keep any annotations, the more effective you will find them while you are playing. For a rigorous analysis of any kind, I recommend that my students use a separate copy than the one they are learning / performing with.

Hello! I’m a “writer” - I remember things better when I’ve picked up a pencil and annotated a score, whether it is for harmonic analysis, keys, or interpretive ideas.  I always use another copy for this to keep my original copy in good condition.  I store my “annotated” scores/copies, and then if I come back to the piece at a later date, either for myself or a student,  I don’t need to work it all out again.