Hmm, you could do it using the multiplayer plugin: http://www.scirra.com/forum/plugin-network-v03a-update_topic43662.html
But you will need to have it running in XP compatability mode and run as an administrator on anything Windows Vista and up.
Here's a chat mmo I made with it: http://www.scirra.com/forum/pixel-people-online-alpha-02-source_topic43970.html
Have the main application run as the server, then have the client automatically connect to it (connect to localhost to run on the same machine).
Otherwise you can try passing a text file between them, have input.txt fed to the client, which then edits output.txt for the main to read. I think you'll need to write/read them at different times in order to prevent them from accessing the same file at once though.