When your card runs out of charge / load you can easily add charge in any train station that you are in, a easy as getting a new train pass, PASMO or SUICA. Generally most stations have specific loading kiosk for each kind of train pass, PASMO or SUICA. But for some stations they have loading kiosk that can charge either a PASMO or SUICA card. You can easily locate this or ask to train station officers.
Commuting by train is very convenient and takes less time compared to driving. Although the trains are really full during rush hour. It is still a good choice compared to driving and getting stuck in the traffic.