I've seen them used two ways, but I'm sure there are a few more techniques out there.
Monotone:
Values of the painting are done in light layers of blackish color, then overlaid with transparents.
The only problem I see with this is being able to achieve realistic shadows with colors like yellow(It tends to look like a dirty green)
Glazing over Opaques: (Glazing what using transparents is called in the hairy brush world)
Opaque paints can be mixed to match color, but end result can look flat and dull.
Transparent paints(even yellow) darken the value of what they are being sprayed over.
Match your opaque colors to the hue, chroma, and value of your target color, and use them for your underpainting. Add a little white to get the value of the color about 1 lower(on a scale of 1-9).
Use transparents to do the final tinting and color shifting. The transparents being overlaid will make the opaque colors darken in value and increase vibrancy.
Marissa is the master at this stuff, see the picture below. It looks like she is using a form of the "Glazing" method(not a real method name, just ad libbing)
Image Source:
http://marissaoosterlee.com