Follow the Laquer, Enamel, Acrylic rule as described in the FAQ. Now with that in mind, there are several ways of doing it.
If the clear is the same type as the paint, you can either shoot clear immediately after the final color coat or wait until the final color coat cures (up to 2 weeks) before shooting clear. If you shoot clear right away, the clear and color coat will gas out and cure together; fine. If you don't shoot it right away and put clear on before the color coat has cured, the clear will be ruined as the bottom layer tries to gas out.
For mismatched paints e.g. enamel color covered with acrylic clear, you must let the color coat fully cure.
For best results use the same type, preferably the same brand. Boyd's clear over Boyd's enamel, for example.
You can even slowly mix clear into your paint as you apply the final color coats. Let's say you plan on putting 10 coats of paint (who really counts these things?). On coat #8, add a bit of clear to it. On #9 even more clear. Coat #10 could use a lot of clear, say 75% clear to 25% paint. Then follow up with the pure clear coats. Only do this with same type/brand paints/clears and make sure they are indeed the same type!
As a side note, pearl colors are almost always duller than solid colors so a clear coat is usually a necessity. Don't buy a pearl color without picking up a bottle (or can) of clear to go on top of it. Otherwise you'll go nuts color sanding and polishing it and wondering why it isn't getting shiny.
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