I use a big spoon, a soft, large make up brush and my ballast spreaders make out of Plastruct sheet plastic whatever-the-Hell-it-is contoured to a prototypical ballast contour stolen from official U.P. documents that you used to be able to download from their site.
I also leave ballasting as the last scenery item to be done after scenery around the tracks is pretty much finished.
Additionally, I screen my real-rock Highball N-scale ballast so most of the dust is gone and the "rocks" are about a scale 3.5" in diameter. I you don't get rid of the dust, scale N-scale ballast has a tendency to look like lumpy concrete. Get rid of the dust, and it looks like real ballast.
I also blend several shades of Highball N-scale ballast together with graded real-rock that I've dug from my LDE real sites to get the blend looking like the gray, black, red-brown, light gray mix that's on the real railroad. A couple of buckets of sacred dirt goes a long way.
Photo (1) - Ballast profile spreaders:Photo (2) - Ballasted and weathered mainline and branchline trackage at Echo Curve:I use various soft brushes to get the small rocks off the tops of the ties and sides of the rails. Lots of work, but well worth it IMO
Cheerio!
Bob Gilmore