What brand / type of paint, and what brand / type of clear? Real Sharpie markers?
Details man... we need details.
Progress! And Details!
Before we get to fascinating interactions between Sharpie and clear coat, the outboard pew-pew sticks are primed. I think I can touch up sand them and get a coat or two of silver metallic on tonight, which means that they'll be ready for Sharpie-ing tomorrow or Wednesday.
On to markers. For starters, the clear coat is Rustoleum Crystal Clear Enamel. All markers are name brand Sharpies, colors as shown below in the pictures. My first round was to make three T-shaped lines with red, green, and blue so that I could establish whether a light coat of clear would make the ink run. Second round today was to make a second line in the same color to the left of the T to establish how much of the color change was the clear coat causing fading and how much was just how the color went on. I also added two new colors (purple and magenta) to see how those perform. I re-coated with clear coat after taking these pictures, though I don't have results photos from that. Results were...
Red and magenta: I thought that the red faded quite a bit with the initial application of clear coat, though the difference isn't super-obvious in the picture. The red seemed much more faded after the second coat of clear. The magenta held color under one coat of clear.
Blue and purple: Blue holds color with one or two coats of clear. The purple was much more lavender when drawn on, and nearly disappeared under the clear coat.
Green: There's an unfortunate reflection of the sun in the picture, but green held color under the one or two coats of clear coat. I thought it went on darker in the first place, but that must have been an illusion. It does go on significantly lighter than you'd expect--this is a standard dark green.
Conclusion: I think there is something odd happening in the CMYK absorption spectrum with the clear coat, since some colors are completely unaffected by clear, and some are noticeably changed. I'm guessing that this is due to whatever Rusto uses to absorb UV/minimize yellowing. I also think it's possible that the clear coat below may change the appearance of the color above.