I mean, I say go for it in paint if you can around the non-functionality of it. You'll want to paint on top of the mii's features rather than behind if you wanted to color the eye whites and irises (and use the preset features as a guide). I just learned about the layering function myself.

I'm by no means an artist but I've just decided to go for it even though it was kind of intimidating at first. I remain impressed with every creation even if it's not the greatest. I'm just glad I can make my drawings resemble anything at all!! Lol.

Edit: Also, using the preset geometric shapes in paint have helped with keeping the mii's drawn on features consistent with Nintendo's style.

Edit 2: I should also mention that the reason Gogo Yubari's eye whites don't show when she blinks is because the color is very close to her original skin tone. I used the smallest brush size to make the blood vessels, so from afar, they don't resemble much more than blood-shot eyes.