To put it in perspective I first travelled to Tokyo in 2000 with my 7 year old daughter, by the second day she was in charge of all subway navigation (deciding the lines we'd take to get from one place to another, navigating within the station when changing lines etc). It's a big system but the signage is excellent and easy to follow. As has been mentioned the key for navigating when you leave the station is to know your exit and one of the things I love about the Tokyo subway system is that the maps at the station you start your trip (for that line) will tell you what carriage is best for the exit at your destination station. Brilliant!

After my first trip to Japan I started travelling very regularly as I was racing cars at the time and it was much cheaper to fly to japan to buy parts and 'suitcase import' them back to australia. This meant travelling out to some pretty far flung places and I managed all of this with the kodansha atlas which has been recommended. No smartphones and GPS, just a good map and some common sense. It's really not hard.

In terms of directions the one bit of advice I give everyone these days is that if they are lost rather than asking someone it's best to stand there with a map in your hand looking confused. If you ask someone you'll get someone who can't understand you, who now has an obligation to help you and will flap about being useless for 30 minutes. Worse than that the person who can help you will see that you're being helped and not stop. By standing there looking hopeless within a couple of minutes someone will stop, ask if you need help and get you pointed in the right direction (or actually take you there, thats surprisingly common).

And finally it's tokyo, not the sahara. The worst thing that can happen is you might need to pay $10 for a cab to get you back to a station, maybe stopping off at an izakaya for a couple of beers and some food. You'll survive.