When dining at a restaurant in the U.S. or other countries, it is customary to pay at the table and leave a tip. In restaurants in Japan, there is a slightly different custom. After you order and all the food is served, a check is placed on the table by staff and you take it to the cashier to pay when you leave. There is no need to leave a tip at the table in any restaurant. It's not rude at all.
Many of the ramen shops and small eateries in town in Japan do not accept credit cards, so make sure you always have some cash on you.