I had the same problem when I first got to Japan, regarding banking. Since no one here could help me, I basically ran out of money and got screwed. Here's what I've been doing and it works with no problems.
Do NOT get a Citibank Japan account. You won't be able to transfer between Japan Citibank and USA Citibank without massive hassle, if at all. Japan Citibanks aren't all over the place either. Japan Citibank and USA Citibank are completely different financial entities. The people at the USA Citibank were either completely ignorant of how banking is conducted in Japan or they flat out lied to me.
Also, Japan Citibank requires a minimum 200000 yen, else you pay through the nose in monthly fees. Banking in Japan is byzantine at best, and in order to pay your rent and get your salary, a Japanese bank account will provide the least problems for you.
Do get a USA Citibank account. You can withdraw from USA Citibank at any Japan Citibank. The savings account (USA) has a low minimum option and the interest rate is good. The unlimited checking account is good too. And you can withdraw at just about any ATM in the USA.
I have a USA Citibank account and a Mizuho (Japan) account. Mizuho has ATMs all over the place. Also, my landlord has Mizuho, as most do, so you just transfer your rent money to the other account with no fees. You can use online banking on Mizuho if you know Japanese, but you can still pay bills at the convenience store too.
I use GoLloyds to transfer from Mizuho to Citibank. That's why they are here. It couldn't be easier. Like, my dog could do it. I do it at least once every two months, to pay loans and for the better USA interest rate. I don't think there is any limit to the amount either; I've transferred about 300000 a few times. And they have a website where you can monitor the exchange rate. When the rate went below 100 yen a few months ago, I basically drained my account and sent it over to the USA.
It costs 2000 yen to transfer regardless of amount, and then $10 is deducted from the USA bank account.
While this seems like a lot, I'd be surprised if any Japanese bank charges less, and the exchange rate with GoLloyds is probably the most reasonable you will find. You figure it costs around $30 to transfer, say $2000; that's only 1.5%.
Also, with GoLloyds, there is a minimum of paperwork. Like, the complete inverse of what you have to fill out with the Japanese account. When I asked about making transfers at my Japanese bank, the minimum fee was 8000 and the paperwork was voluminous. Japanese financial institutions are prohibitive, they aren't going to let their yen out of the country without a fight.
It takes me about 30 seconds to make a transfer to the USA account. I really don't think, once you get settled in and start working that you're going to want to juggle 3 or 4 accounts, or worry about postal orders, and all that.