I will tell you how I handled things when I was there for 2 weeks. This was just a vacation mind you and I had my Japanese friend with me.
I brought a travel card, kinda like a debit card but....not. My mom could put money onto the card for me so I could use it. Easy enough? NO. Japan loves cash, they don't use cards everywhere like we do. Everything is cash, except maybe super markets and some random places. Bigger cities like Tokyo take cards more often but still, never plan on it. Always have cash! It's safe enough to walk around with plenty.
Also, since it wasn't a real card, it didn't work on ATM's. Now, I didn't try the "correct" atm's but I know my card didn't work on them. I was stuck. I had some cash on me but I didn't want to always waste it. Luckily Reiko would pay for some food and such and we just paid her back when we got home.
So, I have been looking into HOW to have money over there for 3 months. I can't just bring a giant wad of Yen. No no. So, I found this site:
http://www.tripadvisor.com/Travel-g294232-s601/Japan:Banks.And.Money.html
It's a trip adviser site but that page tells you how to handle money. Was very useful. Basically, have a card that is VISA, or the other options. I have a visa card and I am going to pray that it works in my favor.
Foreign cards can be used in ATM's found at Post Offices and 7-11's. I am going to take a good guess and say you can always use them in Airports and maaaybe Train Stations. So I am going to bring some cash, exchange it once I am in Japan at the airport and then once in town I will make sure to find where these ATM's are. Hopefully that is easy enough.
I wouldn't suggest travelers checks, they are just a pain. Hey, if it's what you like, go for it.
Also, make sure you have cash on hand for any bills. They don't take checks! Especially foreign ones, haha xD
Hope this helps!
ps. Always remember exchange rate!