Just like you can use Black, White, and Grey, without a hueTo be honest I think it's a bit of both, they tie into the elements sometimes but they can also be used individually. I mean Genjutsu are usually pure Yin Chakra techniques. And the Creation of All Things technique is both Yin and Yang with no elemental chakra at all, Yin to shape it and Yang to form it.
But you can still combine some Red and Yellow to make Orange, then mix in a spot of Black to make Brown… Or add a dash of White to Red, for a Pink.
(Or perhaps it's better to look at Yin and Yang as making up the texture of a base "emulsion" that the Elemental colours are added to, like mixing paint? And then you can add glitter or glow-in-the-dark pigment if you want to represent Natural Energy or "Biju-juice"…)
Actually, I think I've just come up with a better analogy: baking! Yang, being the solid physical energy, is your dry ingredients — stuff like flour and butter. Yin, being the flowing mental energy, is your wet ingredients — water and oil. You can use both sets independently, but for the best results you normally want a mixture. More Dry than Wet results in a solid dough, with which to make crunchy biscuits. More Wet than Dry results in a soup or a gravy. Somewhere in between lies batter, for making nice fluffy cakes.
Then you add some chocolate, or a dash of vanilla essence, perhaps some coffee or some cinnamon, which represent the Elements!