Application behind menu bar.

If this application - which shouldn't be behind the menu bar in the first place - doesn't show a 'Windows' menu in the Macs main menu bar then it's badly written (I notice it's a beta, which means it's liable to be flaky). Quit it (command-Q) then see if you can locate it's preference file in (user)/Libary/Preferences. Move this file out to the Desktop and restart the application. You will need to re-enter any settings.

Try this: Click on your application to bring it to the front; hold down the option (alt) key; click on the 'Window' menu and select 'Arrange in Front'.

There should be a 'Window' menu in the menu bar at top of your screen unless your application is not observing proper standards and hasn't provided it. You need to hold the option key down while clicking on it in order to see 'Arrange in front'.