I don't know anything about applying this mod, but if you need to run a command in the same way as the Windows Command Prompt, you can use CrossOver's Run Command dialog with the command "wineconsole cmd" (without the quotes). That will give you a command prompt window. It should work like on Windows.
Alternatively, you can just pick the .exe file using the Browse button and then insert "wineconsole" in front of the command that gets built for you. The wineconsole program creates a console window and then runs its argument (another program) in that window.
Finally, if you need yet a third way of working, you can toggle open the Debug Options section of the Run Command dialog and click Open Shell. This will launch Terminal, open a new window, and configure that window for working with CrossOver and the selected bottle. After that, you can issue "wine" commands in that window.