When I run wineprefixcreate I only get two drives, c: and z: (which maps to /). Should there be a $HOME drive mapping, and should I point the "my documents" directory to that instead?
Yes, I think that'd be a good idea.
In theory My Documents can be controlled by the registry. In practice I think quite a few apps hard code it. So maybe we could make My Documents a symlink to Y: or whatever we use as the home drive.
Currently symlinks are disabled by default in case of loops. I think we could have some smarter logic to detect that case though, then we could make sure every app which used My Documents was really looking at the UNIX home directory.
wineprefixcreate needs a fair bit of love actually. Right now its drive detection code is rather poor, and there are various packager-specific patches floating around to improve it. These should be moved upstream.