I used a small cheapo artist's paint brush with the bristles cut short to stiffen them a bit. I used the shake-the-bottle Floquil "Rust" and also Poly Scale's "Railroad Tie Brown". The former is oil based, the latter water based, so different cleanup required.
It goes much more quickly than ballasting, so I don't mind painting rails. You only have to paint the sides that get photographed or viewed, too.
You can teach yourself how to apply the paints this way. It takes desire, first and foremost, and then time so that you can relax enough to actually enjoy this for about 10 minutes at a time.
Hints - every three or four minutes, clean off the bottle neck, close up the bottle, and give it another shake. Your paints will be nice and thick this way.
For Floquil especially, do take the time to meticulously clean the threads and inner faces of the cap, and do clean the outer neck and threads of the bottle before you cap and store the paint. Or else...!
-Crandell