I bought an IDE to compact flash converter from eBay... There was a set of instructions on how to set it up using WinUAE on the PC which I followed, but as far as I can tell it's just as easy to plug it in (making sure the red end of the ribbon cable is to the BACK of the Amiga case, not the front, which caused me no end of problems) and just run HD Toolbox from your 3.0/3.1 Install Disk as-is - the card gets treated just like a Hard drive.
Does anyone know if any of these dual IDE-CF adapters (i.e. one which takes two cards) work on an Amiga? I'm getting brave now and considering two 4Gb cards
Oh, and I can second the comment about the Transend 4Gb card - that's the one I use. Lovely.
-Peter.