Well, if you don’t want it to look like a rainbow puked on your note sheets, then you should used a plain pen to take your notes, and then highlight it with some color. Let’s see what I do:
As you can see, I used a plain pen (just a simple blue bic byro, no fancy pens) to take all my notes. Then, I used a bit of color to highlight important things, but when I’m highlighting my own notes, not printed ones, I like to use normal colored markers, because it looks more neat and not so brightly colored. I only use the highlighters with printed notes and books. However, this is what works for me.
If you have to paint graphics, diagrams or that kind of thing, I would suggest leaving a blank space beside the explanation of that draw. In physiology, our professor explained every graphic, so I just wrote down the important things about the explanations and then I painted the graphic or diagram myself. That way it looked better and I could have both things!
Just try and see what is better for you, I used to take my notes with different colored pens at the beginning, but it took up much time, so I simply went for the blue gyro and then I colored it when needed. I also use pastel colored markers, like blue and pink and yellow and soft green, because otherwise they look too strident for me, but there are people who work better with neon highlighters, so that just depends on you!
Using small colored post-its, like the ones you see in the photos, can also help to make your simple notes into a more colored and appealing thing, I just love post-its!!!
Hope this helped at least to give you some ideas!!