As Griff said, if you wrote the console application, then your best choice is to alter it so that it doesn't prompt for input.
If it is not something you can change, then maybe it already has something like that. You should investigate it further.
Failing that, you can write a console application which runs the application via a Process, detects the prompt, and responds to it. This doesn't always work, but you can try.
I have done this sort of thing :
ProcessCommunicator[
^]