I used brads on my layout to fasten the track to the homosote (they also serve to fill those holes!). I don't ballast my track the first year after laying it. With a large expanse of benchwork (2400' of track) I've found seasonal change can require minor adjustments to the track - much harder to do once the track and ballast is glued down. For best holding power and appearance I prefer brads with a slightly tapered head so they "swedge" flush into the ties strip without downward distortion when pushed home . However tapered head brads are getting hard to find. The Chinese brads I've found lately don't have tapered heads like the US made ones I started the railroad with. With step head Chinese brads I countersink the hole in the plastic tie strip with two twists of a hand drill.
After painting and weathering the brad heads virtually disappear.
Ed Rappe