First heed JBI's information on externals. It's no place to run programs.
Second, you can install wine in different locations. By default the user has a .wine directory where Windows applications are installed. However, you can create as many of these directories as you want. This comes in handy because if you are like me and you have Windows games that you play in Linux, each will require different dlls. It's easier if you keep them separate. I usually install things with a 32-bit prefix for maximum compatibility so something like this at command will allow you to create new wine locations (it will create the final directory for you by the way -- let it).
WINEARCH=win32 WINEPREFIX=/path/to/your/location winecfg
If you want to reference/hold that location to run a program put this in first:
That usually gives me problems because the windows locations are hella long and have spaces in them so when i go to initialize a program I always get the spaces wrong. So now I just call the programs from the particular location like this:
WINEPREFIX=$HOME/STO WINEARCH=win32 wine "c:\Program Files\Cryptic Studios\Star Trek Online.exe"
Your Wine Prefix is basically the location. Hope this helps.