Depending of your destinations, you might have to use bus network, especially on the west part of Tokyo. There are different compagnies as for exemple the one between airports (Narita / Haneda) and city center. If you wanna travel with nightbus, I used Willer Travel. The main advantage of using bus is it lower price.

Toei bus:

• Location: Tokyo center
• Price: fixed at 210 yens 
• Usage: Get on by the front door and pay directly when you get on bus. Once you want to go down, push buttons located closed from seats and go down by the back door.

Suburb bus :

• Location: Tokyo suburb
• Price: variable depends of the distance (as trains or metro)
• Usage: Get on by the back door. If you pay by coins; take a ticket; otherwise swipe your IC card on the sensor. Once you wanna go down, push one of buttons and go down by the front door. If you pay by coins, the amount to pay will be on the screen of the bus front; under the number (the one you have on your ticket). if you pay by IC card; just swipe your card on the sensor.

Payment method: IC card (public transport card) / coins