You will need a Japanese bank account to receive your salary from IPMU. You need an Alien Registration card to open a bank account (a temporary one may do this job). Probably the most convenient bank to have an account of is Sumitomo Mitsui Banking Corporation (SMBC), because it has an on-site ATM. You also find ATMs at most convenience stores (e.g. Family Mart close to IPMU). The fees to use these ATMs are waived for most major bank accounts if you have direct deposit. IPMU will provide a person to accompany you to the city hall and the bank as the paperwork must be done in Japanese.
Citibank Japan offers the best deal and flexibility with international transactions in general. With their ATM cards, they use the TTS (Telegraph Transfer Selling) rates and charge no fees if you use Citibank ATMs in the US. You can also maintain accounts in other currencies. They have a checking account in US dollars from which you can withdraw US dollars at the US Citibank ATMs without any fees. However, they have a hefty minimum balance requirement to avoid monthly maintenance fees, 500,000 yen or $2,000.
Both Citibank and Shinsei Bank offer online banking in English. Shinsei Bank has a branch close to the Kashiwa station. Citibank does not have a branch nearby, but has a branch in Ginza open 24 hours and also an extensive telephone banking service. You can avoid fees to use ATMs at 7/11 convenience stores if you maintain 1,000,000 yen minimum balance.
Japan Post Bank ("yucho bank", rapidly expanding banking branch of former Post Office) can be used for direct deposit of salaries, but not for travel reimbursements due to a reason yet to comprehend.)
If you frequently travel outside Japan, you probably want to have ATM cards that can be used outside Japan. Most major banks do offer such cards with the Plus or Cirrus network, which you need to apply for separately from the usual ATM card. Find out the fees associated with such a transaction.
Note that bank accounts in Japan do not allow you to write personal checks. If you need to send money elsewhere, you use either wire transfer or send a bank check.
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