To access and deposit files onto your HDD indepently, just use Windows Explorer. Ephpod does not do this for you though, it only manages mp3s, and puts them in multiple folders. So if you want to store other media files or documents, use Windows Explorer. You should be able to see a 'Removable Hard Drive' in your list if HDD in Windows Explorer and its a matter of simply draging, or copy and pasting into that drive.
It's as simple as that.