Individual Locations

• Tokyo
• Osaka
• Kyoto

On Suica

If you have an iPhone, you can add a digital suica, which is the transit card for almost all of Japan, with apple wallet. This is easier than the physical card, because you can only add money with the physical card with cash.

Online Payments

Credit cards require 3DS support, which many American issuers don't support very well. Ironically, American Express is one of the cards that will generally work if accepted, as they do handle 3DS reliably.

Shinkansen Tickets

Each JR has their own website. Tokaido (Tokyo <> Osaka) is smart-ex, JR East is ekinet, JR West can be found here.

Do I need a ticket for the train

If the train doesn't say anything, no, just use your IC card.
If the train says LIMITED EXPRESS - then yes, you will need a seat reservation, which you will typically have to buy at the station.
If the train is a Shinkansen - then yes, you will need a separate ticket. The seat reservation is a separate ticket from the base fare, if you choose to get one.

Paying at restaurants

Usually, the waiters will bring you a bill when you're finished ordered. You will take that bill to the register at the front, instead of having the waiter collect your card like in the US.

Conbini Script

The first question they will always ask at the register of a conbini is whether or not you want a bag. If you want, listen for "fukoro". If you're buying food, then the next thing will be whether or not you want them to microwave it (listen for "o-bento"). Sometimes they ask about point cards, which just sounds like point card but in katakana.

Subway

You're supposed to be quiet on the subways, so try not to chat, and you're not supposed to eat food or drink.