Use really small nails and you should have gotten a crayon with a touch up pen. If not, you can order both through HD or Lowes. You can probably get filler anywhere, but the touch up pen will be harder as the formula is specific to KM (I tried as Mohawk makes it for them).

My cabinets were just installed this week. I don't have crown molding, but I do have flush trim up to the ceiling. The way they did it is to attach another piece of stock to the back of the trim piece, that rests on the top of the cabinet. Then they screwed up through the top of the cabinet into this. There are no surface nails on the trim at all.

Elsewhere, in a few places when they couldn't avoid surface nailing they used a little nailer that drives pins the thickness of needles, that don't require any filling at all.