The colour primer you use as a base depends on the colour of the flakes and the effect you are after. The base colour effects the final results, which is why manufacturers colour samples usually show the flakes over different bases. the same goes for pearls. In the past flakes were mixed with the same clear as your top coat, but theses days there are also specailty clears designed as carriers for flakes to help them lay down flatter so you don't need to use as many coats of topcoat to bury the edges of the flakes.