A WINEPREFIX itself is a different '.wine' directory and you create a new prefix by setting the WINEPREFIX environment variable. E.g. WINEPREFIX=.wine-notepad wine notepad would create a new prefix /home/user/.wine-notepad for notepad. It would also be possible to have multiple wine installations but for that you need to play with other environment variables like WINEDLLPATH, WINELOADER and WINESERVER next to things like PATH.
