Add the CF card as a drive under the WinUAE "harddisk" settings. Boot with the WB 3.1 "install" ADF, and launch HDToolbox. (First, you will probably have to change HDToolbox tooltype from "scsi.device" to "uaehf.device".) You should then be able to partition the drive with HDToolbox, reboot, format, and install 3.1 from the ADFs.
I'm sure others will pop in with anything I've missed.
