@kyondayo Besides making sure you have a US account set up before you leave, it might be good to talk to a CPA/tax prep person before you leave about your prospective US tax filings and maybe use that person for the first year, maybe two, that you're here.
In general terms, the US requires you to submit a yearly tax return (and pay tax, if that's how the numbers turn out), but the US also allows expats to claim a generous exemption--I think it was just over $101,000 for the 2016 tax year. This is called the Foreign Earned Income Exemption (FEIE) and if you google it, look for IRS form 2555 and its instructions. I think the vast majority of US expats don't make more than $101k, so filing is more like a formality--you very likely won't pay US taxes.
For tax prep, I've used Turbotax (TT), then a CPA for a while (due to owning some limited partnerships--a tax headache), and recently switched back to TT, which works fine.
In your case, you may end up straddling a tax year--in a calendar/tax year both time in the US, and time in Japan, maybe working in each period. The FEIE allows you to claim a partial year (part of that big exemption), but I'm not sure how well TT handles that, which is why an in-person CPA might be good for your first year (or two) that you are here for US tax filing. Once established and past that quirk, you'd be able to do it on your own.
The other thing related to this is deductions that your US employer might make. As a US resident, there's probably SS, some withholding, etc., but once you've established residency in Japan, they should stop doing that. If your employer is experienced with telecommuters overseas, good; but if not, they may need some convincing.
On the Japan side, once you are a resident, your worldwide income is taxable (as are capital gains & dividends), regardless of where it is paid (and regardless of whether it is repatriated to Japan or not). You're a resident here, so you've effectively worked here, or from here.
Blah, blah, blah...
