It is considered to be rude to count the change that has been handed back to you after making a purchase. This is a culture that prides itself on its honesty — it’s better to be trusting (plus, are you really in a position to translate the currency quickly enough to make this assessment?).
Credit cards are accepted almost everywhere, despite the fact that Japan is generally a cash-based society. ATMmachines are also widely available. Play it safe — before leaving home, visit your bank and change your PIN to a 4-digit number; we learned the hard way that not all machines around the world have the fun little letter/number combination on the keys or that they only accept 4-digit PINs.