Here's how I did it:
- Start winuae with the disableharddrivesafetycheck option ,for example "C:\Program Files\Cloanto\Amiga Forever\Emulation\WinUAE\winuae.exe" -disableharddrivesafetycheck
- Load your config and goto the harddrive section and choose addharddrive. Select the cf card. Don't forget to select the read/write option.
- Start emulation.
- Start hdtoolbox (set the Device tooltype of hdtoolbox to uaehf.device)
- Install and partition the CF
- Reset the system
- (Quick) Format the CF
- Copy all the files you need to your CF
- Install the cf in your a1200
One thing: I did this under the 3.5/3.9 environment of Amiga forever 2006.
I also tried it with a os 3.1 environment, but with hdtoolbox of 3.1 (and also hdinsttools on aminet) it was impossible to partition the cf card.
Hope this info is of any help.
Edit: Edited some small things to be more clear.