If you are using wine installed from the repositories then wine related files is stored in a folder called ~/.wine
Windows programs are stored within this folder – for example :
~/.wine/drive_c/program_files/Internet Explorer
You can start a windows program in a similar way as from a command line in windows but prefix it with wine
wine "c:\program files\internet explorer\iexplore.exe"
References
https://askubuntu.com/questions/65487/invoke-a-wine-installed-application-from-command-line