Touch-up pens - is there a trick to this?

[Rizzo]

I recently got a touch-up pen from the dealership and covered up a few nicks from highway driving. I did the clear coat bit, too.

The marks are less noticeable, but with a larger chip I can see the new paint I put down as a darker patch. Strange thing is, there are a couple of chips on the corner of the door that covered up just fine, so I know the paint is matched correctly. Did I put it on too thick? I would've thought that would make a bubble of paint, not a darker area.

Also, with the smaller marks, I can see the clear-coat on it as an extra layer over the original paint. It's frustrating that it doesn't just level off somehow. I feel like the world's worst artist when trying to touch up the chips. Is there any trick to it that I should know?