This sounds like quite an undertaking. I have built a model subway (actually it's all elevated because if it were subway, no one could see it), in my basement. It is my version of a model railway, but instead of mountains, tunnels, etc., I have built a large urban centre with bridges, expressways, and of course, rapid transit. This has been a work in progress over the last several years, and I actually had to move the entire thing from my old house to my current one back in 1991 (so now a lot of the streets look like true city streets - broken pavement, etc.!)
Anyway, it will one day be fully electric and the trainbodies will have to be all hand made. It's in (more or less) N-scale. A true labour of love, as you can see.
There will eventually be seven routes, although some use the same rights-of-way. Two main city centre routes have express and local tracks, while the suburban portions have either two local or two local and one peak express. While the city is ficticious, this system is more or less designed to reflect the style of our favourite system: New York's.
Feel free to e-mail me for more information. I'd love to hear more about your endeavours in this, what sounds to be colossal, undertaking.