I have little experience with WHS' remote file access. But I suspect you'll want to use another connection method to upload large numbers of files or entire folder structures. WHS (Server 2003) can act as a VPN (PPTP or L2TP) host or yoi could use another remote connection/file transfer method.
If you are talking about a completely independent file structure (not part of the WHS storage pool), then you could add a separate hard drive and not add it to the storage pool. Then you could directly share the disk to your network. Again, you'd need to use a VPN or other remote access method to access the shared disk.