You need to use transparent paint when painting over foil in places you want it to "shine". Opaque colors are used where you don't want the foil to show through. The transparent paint allows the foil to remain reflective as some light is still allowed to pass through the paint. As far as coating the foil before painting that is to give you a smooth surface to paint on. Coating with epoxy hides the edges where the foil stops. After foiling I give the bait a coating of 30 minute epoxy. The epoxy dries clear so it doesn't interfere with the reflective properties of the foil. Some people skip this step entirely and go straight to painting. I like the fact that the epoxy coating gives me a smooth surface to paint on and there are no visible lines where the foil ends.
Ben