You have a virtual filesystem in your uaerc configuration:

#filesystem=rw,Data:sys:emulation/e-uae/HardDisks/Data

Erase the # and when you will launch WB 3.1 you will have the System folder (with 3.1 installed), which is phisically inside the hardfile and the Data folder, inside sys:emulation/e-uae/HardDisks/. This folder is normally usable inside Ambient (is a real folder) while hdf file is a raw data file and you can't read inside with a double click (if you try you will receive a "No hexview for..." message). But when you launch e-uae this file is normally readable/writeable.
If you insert any data inside your real folder (called Data in your config) when you will start WB 3.1 you will be able to read/copy/write in both folder, System and Data and this will allow you to exchange files from Data to System.