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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.
Good for you. If you don't know about it, you can also use tab completion. Type the first few letters of a file or folder and hit the tab button, and bash will autocomplete it for you. If the file name has a space or other illegal character in it, it will automatically escape it for you.
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