That wouldn't be good enough, you'll need a DOS bootdisk (i.e. where Windows isn't loaded at all).
Once you've got that created, copy the flasher tool + firmware to the disk and reboot.
Hopefully the PC will then boot up from the floppy and you'll hit the same sort of command prompt.
Then type in...
DWL X 107.hex /M
where 'X' is a number between 0 and 3, depending on where your drive is positioned on the IDE BUS.
0 = Primary Master, 1 = Primary Slave, 2 = Secondary Master, 3 = Secondary Slave
The BIOS screen might help you figure out what it's connected to.
Also, if the drive is on a totally different cable to the HDD then it's probably secondary something.