I don't recall Wine installing files to the root folder. It installs files on a hidden directory in your home folder. Press Ctrl+H in your file manager to show hidden files and folders.
What you call administrator is not root under Linux. The root user is allowed to do everything, the administrator just has privileges to run programs and command as root when needed. Depending on your desktop environment and file manager you use (it helps to provide details when you ask questions), there are various ways to do that. In Nemo on Cinnamon, it is even easier than nomko suggest, just right-click a folder and from the context menu select "Open as Root". After you have authenticated yourself, Nemo will get the permissions from you to open the folder as root.
Linux Mint 14 Nadia / 64-bit / Cinnamon