You should be applying it in one thin even stroke with a wide flat brush. If it is still running the inks, it's too heavy a coat. Never go back over it again untill it's completely dry. One coat is normally enough though.
Edit: Just read your other post. You didn't say you printed them yourself. That is a diffrent ball game now. You need to spray the markings with a clear enamel or laquer. Any water or alcohol based clear (including the decal film) will re-disolve the inks.