Ok, first of all, relax. It's not that difficult. the ~ just represents your home directory, so it's the equivilent of /home/username/. Files that begin with a dot are "hidden" files, ones that don't show up on a regular file listing. In a console you can list hidden files and folders with "ls -a". Your gui file browser should also have a command somewhere to show hidden files.
Now wine is a bit different from most programs because it's a *nix proram, but it also has to pretend to be a Windows machine to the programs it runs. The actual physical installation of programs by default is a fake windows directory structure located in ~/.wine/, a hidden directory in your home folder. You can change this if you want though. But from within wine, this directory structure appears to be a Windows machine to the programs it's running.
So you can actually run programs two ways. You can use the actual location: wine "~/.wine/drive_c/Program Files/Miranda/Miranda.exe", or you can enter it as a Windows path: wine "c:\Program Files\Miranda\Miranda.exe". Changing these to whatever the real path is, of course.
I hope that clears it up. You can check out this previous thread about creating desktop shortcuts for wine apps: http://www.linuxquestions.org/questi...d.php?t=477527