Greetings,
I am new to handlaying ties and track so I hope more people respond.
I have colored my ties two ways. The first was to paint them after they were glued down as you are thinking. I used the Floquil paint pin that is "tie brown". It was short work to go over the tops of the ties. After the paint dried I went back over random ties to darken them with a second coat. The drawback to this is that the paint only get the tops of the ties and the outside edges. The inside did not get paint but that was covered with ballast. You can see the result in this vid. testing a turnout.
http://www.youtube.com/watch?v=8rPbzPeTvr8The other way I have colored the ties was to stain them. I did this for a bridge I am currently working on. Each tie had to be 16" on center and I knew painting them was not going to be possible. I poured a bottle of Floquil tie brown into a larger container and then thinned the paint with airbrush thinner. This made a wash. The ties were all placed in the wash, the lid was placed on tight, and the wash was swirled around in the container to soak the ties. After approx. two min. I took them out and put them on a paper towel to dry overnight. The next morning I decided to repaet the process to darken the ties. Once on the model I took a micro brush and dipped it in the wash and used it to darken some random ties even more. The disadvantage to this process was having to repeat the staining process. I do not think I would extend the soaking time as I do not know if the wood would swell or warp. Sorry no pics. yet.
Christopher