Hi Matt,
As Sam described, you can substitute the rail without much trouble. The ScaleTrax rail is a loose fit, but a little super glue will take care of that.
In this case, however, we went the extra mile and built a new wood deck using O scale ties from Right-O-Way. One of our scenery artists, Jen Theroux, made a jig to assemble the ties into panels that match the dimensions of the Atlas plastic ties panels. She "creosoted" the ties ahead of time with acrylic paint, and then spiked the ties to a couple boards on the outer edge.
Here you can see one of the wood panels between the stock plastic panels.
Once the ties were all down I spiked ScaleTrax rail using Xeron spiking pliers and Right-O-Way spikes. I also added code 148 guard rails for extra realism. In all its was somewhere around 1200 spikes!
I painted the steel work flat black, added a light weathering with acrylic paint and alcohol, and called it good.