What do you need to once again transfer files from PC to Amiga? I started off with just an internal CF<>IDE adapter for my Amiga, which I would switch between the Amiga (which it would boot from) and the PC (which WinUAE could access) to transfer files.
I've now managed to get a PCMCIA Compact Flash reader + drivers for the Amiga. It can read FAT formatted CF cards, which makes file transfer much easier (and means I don't have to shut down the Amiga and open the case when I want to transfer files, plus I don't have to load WinUAE every time).
If you format a CF as a dedicated hard drive in WinUAE (you need to run WinUAE as administrator) and install Workbench, you can boot a real Amiga from it. You can also take an image of the CF card (using a util called dd.exe, which is a port of the UNIX 'dd' command for Windows) which WinUAE can use as a hardfile.
There are a number of other solutions for file transfer as well. Let me know if I can help.