Well, stick to SFS.
When I load Workbench3.0 from the original disk, I can access all of my 9,1 GB hdd space. You just need to install the filesystem on the of rdb of your harddrive, and I'm sure you can read about it in the manual.
Allso try downloading hdinst.lha from Aminet. It's a HDToolBox replacement, and it's much better than HDToolBox from the 3.0/3.1 Install disk.