you need to sand the surface of the flaked clear smooth, after it dries of course. then apply whatever the specified number of coats your clear calls for w/o the flake mixed in for the final, finishing touch.
Make sure you don't put a basecoat paint between the two it'll react on you if the first clearcoat isn't fully cured. that's why i use sg100 for my flake. some clearcoats it might not react on, but i don't know. it's just my experience w/ it.