I'm only guessing as I don't use third rail on my route that you would go into track network editor mode and In the ribbon loft descriptor if you choose the dropdown icon I would think you'd pick your track choice there, by typing in the track from the route you want to use for example Bakerloo. I could be wrong though.
I just found what the problem was. If you make a marker and select a track you can choose on what side you want the 3rd rail on.