I figured out how do it in vista:
auto load the driver (only has to be done once, in win2000 it only works if I don't install the driver
)
load the software
plug the flash cart into the writer
plug the writer into the usb interface
add the roms
choose to write the roms
unplug the writer from the usb
plug the writer back into the usb interface
click ok at the PC-E/TG-16 screen
your card will now write