The Windows shell (assuming you're using CMD.exe) uses %ProgramFiles% to point to the Program Files folder, no matter where it is. Since the default Windows file opener accounts for environment variables like this, if the program was well-written, it should support this.
Also, it could be worth using relative addresses. If the program you're using is installed correctly, it should already be in the Program Files folder, so you could just refer to the configuration file as .\config_file.txt if its in the same directory as the program, or ..\other_program\config_file.txt if its in a directory different than the other program. This would apply not only on Windows but on almost every modern operating system, and will work properly if you have the "Start In" box properly set, or you run it directly from its folder.