First rule is to choose a specific color for a specific thing and stick to it. For example, always use yellow to highlight dynamic markings and changes within the piece. Maybe you could use green for tempo markings. You get the idea.
Color Coding Your Piano Practice
If you have 2 different melodies or musical themes in your piece this technique works very well. Use color to label musical elements such as Theme A.
Theme A (or the first melody line) will probably be both at the beginning of your sheet music as well as again after Theme B. Labeling each instance of Theme A and Theme B also helps you recognize which measures are exact repetitions of previous measures.
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Using Color to Track Success Points
Try using color to track success points within each piece of music Practicing Section A and playing it without errors is a Success Point. Use a blue marker and create a circle at the beginning of Section A to represent that success. You will quickly recognize it again as you use this same symbol and color in another piece for the same purpose.
Use the colored dot method to quickly look at your piece as you are learning it. Then recognize the different points of success as you achieve them.