I have the dupli-color, and used it to take care of the little paint chips when I first got the Voy. It was a good match - I do have a dark color (graphite metallic, since renamed (?) to Spiral Gray Metallic), but the metallic factor matched up well. I do think it's easier to use touch up / hide the blemish with darker colors vs. lighter, and with a metallic vs. solid color. Has lasted well so far, but I haven't had the vehicle a year yet (I do keep it parked outdoors 100% of the time).
The current pens have the clearcoat in a reservoir on the other end - as the others have said - put that on after the base coat dries. Love the pen applicator vs. the brush - much more precise for me, at least. But it has the brush as well, IIRC, for the larger jobs.
I know my Honda-branded touch-up paint has both pen / brush - but by comparison - my S2K had a solid color (red), and I 'knew' where the touched-up places were on that car, when i had it. I 'knew' pretty much everything about that car, though
Good luck, whichever way you go!