If I have the chance I'll give the software a test run this afternoon to see what it looks like. Then I can recommend how you can run it hidden (it's a small edit to a plist within the app)

EDIT: Ok, it's easy to hide the program's dock icon and prevent it from showing a menu. This is done by editing its info.plist to tell the OS that the program is a background process.

However, there isn't a way to hide the program's UI as easily. I'm going to look into something for that in a second though, just after I reinstall the Apple Developer Tools (new system).