1. Change whatever.exe to accept command args, and then have the Java wrapper do the same, constructing a command line that includes those args.
2. Replace whatever.exe with a batch file that uses positional parameters and pass those as arguments via the Java wrapper.
None of the process streams are related to how the process is executed. They represent the STDIN, STDOUT, STDERR of the process itself. So, if whatever.exe listened to its STDIN in a loop waiting for a "command" that included your arguments, you could do this as a variant on (1). You see this a lot when implementing a native IPC arrangement that doesn't rely on platform specific IPC. Likely overkill for this purpose.