http://www.gregdonner.org/os39faq/installtips.html#12(#12 in above link)
Idea being that when you boot your emergency disk and hold in the left mouse button it will run ATA3Prefs. You then save the correct settings (it'll save them to the floppy) then it'll continue with setup. Obviously next time the boot disk boots you won't have to hold the left mouse button in as the correct config will be loaded when the driver is run.
I have a FastATA, but I don't use 3.9 so I've never had to install the OS from CD to a real Amiga.
Edit:
Those instructions in the link refer to incorrect (old) files. I believe it's ata3.driver, and ata3prefs, but check your FastATA floppy for correct filenames (my Amiga still needs a PSU or I'd check). Just manually copy those files onto (a copy of your) emergency disk into C and Prefs respectively, then use Ed or some other text editor to modify the startup-sequence (as per link but with correct driver and prefs filenames.