It may look insanely intimidating, but is not really that hard to get around it. The ticket vending machines at the Tokyo subway stations are things you should get familiar with if you expect to travel economically within this city. Economical with respect to the taxis there, but not really economical in the true sense of the word. The minimum fare when i was there last year was 160 Yen which comes to around Rs. 95!
With as many as 13, yes THIRTEEN different railway lines, the metro is indeed the best way to get around Tokyo. And don't sweat if you have a hard time finding your correct station. I was helped out by the locals, on three occasions in two days, without me even asking for help. People in Tokyo are really really helpful and will go out of their way to ensure you get the right ticket for the right location. Some will even escort you to the correct platform and see you off. This happened twice with me.