Commander will indeed control your FT-900. Its part of the larger DXLab suite of freeware applications that can be run individually, but when run simultaneously sense each other's presence and interoperate automatically.
After you've gotten comfortable with Commander, take a look at www.qsl.net/dxlab
-- you'll find support for logging, DX spot collection, propagation forecasting and monitoring, a world map display that shows the solar terminator and beam headings and can control your rotator, soundcard digital modes (PSK31, PSK63, RTTY), and QSL route discovery. All of these applications are free.