Depends on the size of the flake. I find no problem clearing over the standard "F" series flake from HOK. I usually candy over them not add the flake to the candy), then clear over the candy.
I have a beautiful one coming up. I'm sure the pictures won't show it (flake jobs are hard to get good pics), but it is candy tangerine with a bright orange outline and candy orange flake flames. Should have pics up in the Samples of Work today (Wed), or tomorrow.