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Either way is acceptable. though I incorporate them with a full repaint if possible, (you won't feel the flames). You can prep the old finish to accept the new artwork, then clear the refinished area, preferabaly the complete panel.
With 3 stage paint the metallic base coat(s) are sprayed, followed by the ghost flames. The candy coat(s) are applied, followed by several coats of clear. On mine, the ghost flames are done in a color that is very similar to the candy coats. I also have shaded flames that are several different colors, predominately blue, orange, and dark silver. These colors show up alot more under the red candy. The ghost flames are hardly visable unless you come up to the paint or see it from an angle. Here is a couple of pics. Hope this helps.
The orange and yellow metallic flames are barely visable under the candy red, you have to be close to see them. The other colors are what show up as the shaded flames.