I've just laid down my 1st loop of track on my layout using Atlas track. I soldered to the bottom of the track joiners. I took fine sandpaper and removed the black from the center rails and just scuffed the outer rail joiner. I tinned the wires and the joiner, and then soldered them together after I bent the wire at a 90 degree. Now the wire goes straight down from the joiner. When I lay the track, I figure out where the wire is going to go and drill a hole just barely big enough for the wire. I feed the wire down and then join the track. It is a bit hard as you don't get much play with the hole so small, but there is no evidence of wires at all when I am done. This should allow you to add new wire holes without much work. Here is a photo two of the rail joiners have wire soldered to them.
