Wine directory structure used in Fedora Core Linux:
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\${HOME}/.wine/drive_c is the root directory (aka C: drive) wine looks for by
default. It is created with (empty) C:\windows and C:\windows\system
directories, needed to operate Wine without an existing Windows
installation, if it doesn't already exists.

If you want to use Wine with an existing Windows installation that is
mounted, for example, in /mnt/windows-c, change the symlink
\${HOME}/.wine/dosdevices/c: to point to /mnt/windows-c instead of the
defaults set by installation.

If you do this, you can safely remove \${HOME}/.wine/drive_c.
(Alternatively, just mount your Windows partition to \${HOME}/.wine/drive_c.)