Talk to the teacher, don’t do this over email. Say you find the note taking format really complicated. Ask which are the most important parts to get partial credit if you can’t keep it all straight.
Ask how it’s worked in previous years: do students catch on? Feel free to raise your hand in class when you are comfused and ask what color you’re supposed to be using if necessary to give the teacher an understanding of where you are struggling.
It sounds like you are allowed go back and mark colors later. You might try: take your notes in pencil, erase and fix as desired after class, then scan the notes and turn them blue, print the blue version, and grab a set of colored markers and underline/highlight stuff in rainbow colors.